Methods and compositions for delivery of molecules and complexes to reaction sites

ABSTRACT

The present invention provides methods, compositions, and systems for distributing molecules and complexes into reaction sites. In particular, the methods, compositions, and systems of the present invention result in an active loading of molecules and complexes into reaction sites with improved efficiency over loading by passive diffusion methods alone.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.16/896,654, filed on Jun. 9, 2020, which is a continuation of U.S.patent application Ser. No. 15/656,622, filed on Jul. 21, 2017, now U.S.Pat. No. 10,711,300, which claims the benefit of U.S. Provisional PatentApplication No. 62/365,630 filed Jul. 22, 2016, the disclosures of whichare incorporated herein by reference in their entirety for all purposes.

BACKGROUND OF THE INVENTION

Techniques in molecular biology and molecular medicine often rely onanalysis of single biological molecules. Such techniques include DNA andRNA sequencing, polymorphism detection, the detection of proteins ofinterest, the detection of protein-nucleic acid complexes, and manyothers. The high sensitivity, high throughput and low reagent costsinvolved in single molecule analysis make this type of analysis anincreasingly attractive approach for a variety of detection and analysisproblems in molecular medicine, from low cost genomics to highsensitivity marker analysis.

The small observation volumes often used for single molecule analysismethods are typically provided by immobilizing or otherwise localizingmolecules of interest within an optical confinement reaction/observationregion, such as an array of extremely small wells as in an array of ZeroMode Waveguides (ZMWs), and delivering molecules of interest (includingfor example, a template, primers, enzymes etc.,) to the reaction region.One difficulty in performing single molecule analyses occurs in loadingthe reaction/observation region of single molecule analysis devices withthe molecules of interest (e.g., template or other analyte and/orenzyme). Entropic barriers to loading can be significant when attemptingto load large reactant molecules into these nanoscale reaction sites.

While passive distribution methods are effective in ensuring that, inmost cases, not more than a single template or enzyme (or other analyte)molecule is loaded in each observation/reaction volume in an array suchas a ZMW array, it would be desirable to develop methods andcompositions for increasing the efficiency and density of loading insuch reaction sites. The present invention provides these and otherfeatures that will be apparent upon complete review of the following.

SUMMARY OF THE INVENTION

Accordingly, the present disclosure provides methods, compositions, andsystems for distribution of molecules of interest into reaction sites.In particular, the methods, compositions, and systems described hereinresult in an active loading of molecules of interest into reactionsites, resulting in an increased density of loading and/or increasedefficiency of loading than is seen with passive diffusion methods alone.

In one aspect, the present disclosure provides a method of delivering amolecule to a site that includes the steps of: (a) providing a tetheringnucleic acid at the site, where at least a portion of the tetheringnucleic acid is located outside of the site and the tethering nucleicacid includes (i) a first strand comprising a capture moiety at aposition that is located outside of the site, and (ii) a second strand;(b) exposing the tethering nucleic acid to a molecule comprising abinding moiety, where the binding moiety and the capture moiety interactto attach the molecule to the tethering nucleic acid; (c) degrading thesecond strand of the tethering nucleic acid, where the first strandcontains self-complementary regions that hybridize together to collapsethe first strand into a hairpin, and the collapse of the first strandfurther serves to carry the attached molecule into the interior of thesite, thereby delivering the molecule to the site. In some embodiments,the capture moiety includes biotin and the binding moiety includesstreptavidin. In further embodiments, the second strand includes RNA,and in yet further embodiments the second strand includes at least onedeoxyuridine (dU).

In further embodiments and in accordance with the above, the firststrand is resistant to exonuclease, and the second strand is sensitiveto exonuclease, and the degrading step (c) includes applying anexonuclease to the tethering nucleic acid.

In further embodiments and in accordance with any of the above, themolecule is a member selected from the group consisting of: a templatenucleic acid, a polypeptide, an antibody, and a small molecule. In stillfurther embodiments, the molecule is part of a complex. In yet furtherembodiments, the molecule includes a template nucleic acid complexedwith a polymerase enzyme. In still further embodiments, the complexfurther comprises a primer hybridized to the template nucleic acid. Inyet further embodiments, the binding moiety is associated with thepolymerase enzyme.

In further embodiments and in accordance with any of the above, thetethering nucleic acid includes capture moieties at both ends. Infurther embodiments, the capture moieties at the two ends are identicalor are different.

In further embodiments and in accordance with any of the above, thetethering nucleic acid is immobilized to the site by an interactionbetween a capture moiety at one end and an appropriate binding moiety onthe site.

In further embodiments and in accordance with any of the above, thetethering nucleic acid is at least 1000 nucleotides in length.

In further embodiments and in accordance with any of the above, the siteincludes a nanoscale well. In still further embodiments, the site is atthe base of a nanoscale well. In some embodiments, the site includes ananopore.

In further embodiments and in accordance with any of the above, thesecond strand does not include a capture moiety.

In further embodiments and in accordance with any of the above, themethod further includes step (d) immobilizing the molecule to the site.In still further embodiments, the immobilizing includes an interactionbetween a first reaction moiety on the site and a second reaction moietyon the molecule.

In further embodiments and in accordance with any of the above, thesecond strand includes RNA and the degrading step includes applyingRNAse.

In further embodiments and in accordance with any of the above, thecapture moiety includes a scaffold, and the scaffold includes (i) a corewith conjugation adaptors and (ii) multiple arms with biotin moieties.In still further embodiments, the arms include oligonucleotides. In yetfurther embodiments, the oligonucleotides are about 25 to about 250 or50-100 basepairs (bp) in length.

In one aspect, the present disclosure provides a method of deliveringmolecules to an array of nanoscale wells that includes the steps of: (a)providing a surface including a plurality of nanoscale wells, where eachof the nanoscale wells includes an immobilized tethering nucleic acidmolecule; (b) distributing molecules to the surface, such that thetethering nucleic acid molecules are able to encounter and capture atleast one molecule, where that capture increases effective concentrationof the at least one molecule to the openings of the nanoscale wells tofavor loading of the nanoscale wells with the at least one molecule,thus delivering molecules to the array of nanoscale wells. In furtherembodiments, the nanoscale wells further include polymerases thatprocess the tethering nucleic acid molecules such that their capturedmolecules are drawn into the nanoscale wells. In still furtherembodiments, the tethering nucleic acid molecule is of sufficient lengthto have at least a portion protruding outside the nanoscale well, forexample about 1000 nucleotides in length. In yet further embodiments,the processing proceeds until the captured molecules are themselvesimmobilized in the nanoscale wells, and in some further embodiments, thecaptured molecules are immobilized through an interaction between amoiety on the captured molecules and a moiety in the nanoscale wells.

In further embodiments and in accordance with any of the above, themolecules are a member selected from the group consisting of: a templatenucleic acid, a polypeptide, an antibody, and a small molecule.

In further embodiments and in accordance with any of the above, thetemplate nucleic acids include a 5′ overhang and the tethered nucleicacid molecules include a 3′ overhang, such that the capture of thetemplate nucleic acids is by hybridization of matching overhangs betweenthe tethered nucleic acid molecules and the template nucleic acids.

In further embodiments and in accordance with any of the above, themolecules are part of complexes. In still further embodiments, themolecules include template nucleic acid complexed with a polymeraseenzyme. In yet further embodiments, a primer is hybridized to thetemplate nucleic acid. In further embodiments, a binding moiety isassociated with the polymerase enzyme, and that binding moiety caninclude in further embodiments streptavidin. In some embodiments, thepolymerase enzyme is maintained in a stalled state until the moleculesare delivered into the nanoscale wells.

In further embodiments and in accordance with any of the above, there isa cleavable linker between the tethering nucleic acid and the surface.

In further embodiments and in accordance with any of the above, themethod further includes step (c) applying a protease to the nanoscalewells to release the tethering nucleic acid molecules.

In further embodiments and in accordance with any of the above, thetethering nucleic acid molecules comprise a double stranded nucleic acidin which the 3′ end of one strand is linked to the 5′ end of the otherstrand with a hairpin oligonucleotide.

In some aspects, the present disclosure provides a method of deliveringtemplate nucleic acid monomers to an array of nanoscale wells thatincludes the steps of: (a) providing a surface that has a plurality ofnanoscale wells, where each of the nanoscale wells includes animmobilized tethering nucleic acid molecule; (b) distributing a firstplurality of template nucleic acid monomers to the surface underconditions for ligation of the template nucleic acid monomers to thetethering nucleic acid molecules to form ligated sequencing templates;(c) processing the ligated sequencing templates, thus delivering theligated sequencing templates into the interior of the nanoscale wells.In some embodiments, the tethering nucleic acid molecule is ofsufficient length to have at least a portion protruding outside thenanoscale well. In further embodiments, the nanoscale wells furtherinclude polymerases that act during the processing step (c) such thatthe ligated sequencing templates are drawn into the nanoscale wells.

In further embodiments and in accordance with any of the above, thetethering nucleic acid molecules are at least about 1000 to about 5000nucleotides in length.

In further embodiments and in accordance with any of the above, themethod further includes a step of distributing a second plurality oftemplate nucleic acid monomers to the ligated sequencing templates toattach additional monomers to the ligated sequencing templates. In stillfurther embodiments, the method includes distributing a desired numberof additional pluralities of template nucleic acid monomers to formligated sequencing templates that comprise concatemers of thedistributed monomers. In yet further embodiments, prior to eachdistributing of additional pluralities of template nucleic acidmolecules, linker molecules are ligated to the end of each ligatedsequencing template to designate the end of one monomer and the start ofthe next monomer, and those linker molecules may in some embodimentsinclude an oligonucleotide of known sequence. In yet furtherembodiments, the concatemers have a length greater than 10 kb.

In further embodiments and in accordance with any of the above, thenanoscale wells further include polymerase enzymes, and the processingis accomplished by the activity of the polymerase enzymes.

In further embodiments and in accordance with any of the above, theligated sequencing templates further include a hairpin loop at one end.

In further embodiments and in accordance with any of the above, thetethering nucleic acid molecules are immobilized to the base of thenanoscale wells through association with a polymerase immobilized at thebase. In still further embodiments, the polymerase is maintained in aninactive state until processing step (c).

In further embodiments and in accordance with any of the above, thelinker molecules are distributed to the surface along with the templatenucleic acid monomers, and the linker molecules and the template nucleicacid monomers have complementary overhangs, to form ligated sequencingtemplates that comprise concatemers of the monomers separated by thelinkers.

In some aspects, the present disclosure provides a method ofimmobilizing reactants at the base of nanoscale wells that includes thesteps of: (a) providing an array that includes (i) a plurality ofnanoscale wells, (ii) a solution layer above the nanoscale wells; and(iii) a conducting layer that allows exposure of cathodes at or near thebase of each nanoscale well; (b) providing capture molecules to thearray, where the capture molecules have a pKa near neutral pH and arewater soluble in their protonated form and insoluble in theirdeprotonated form; (c) attaching the reactants to the capture molecules;and (d) applying voltage through an anode in the solution to selectivelydeposit the capture molecules onto the bases of the nanoscale wells,thereby immobilizing reactants to the bases of the nanoscale wells. Infurther embodiments, the capture molecules include chitosan. In stillfurther embodiments, the reactants include polymerase enzyme complexes,which in further embodiments can include a polymerase enzyme associatedto a template nucleic acid which is optionally hybridized to a primer.In some embodiments, step (c) is performed before step (b). In someembodiments, step (c) is performed after step (d).

In further embodiments and in accordance with any of the above, themethod further includes step (e) exposing the nanoscale wells to anaqueous solution with pH less than 4 in order to remove the capturemolecules and reactant to prepare the nanoscale wells for delivery of anew set of capture molecules.

In further aspects, the present disclosure provides a method ofimmobilizing reactants at the base of nanoscale wells that includes thesteps of: (a) providing an array that includes (i) a plurality ofnanoscale wells; (ii) a solution layer above the nanoscale wells; and(iii) a conducting layer that allows exposure of anodes at or near thebase of each nanoscale well; (b) providing capture molecules to thearray, where the capture molecules are water soluble in their chargedform and insoluble in their uncharged form; (c) attaching the reactantsto the capture molecules; and (d) applying voltage through a cathode inthe solution to selectively deposit the capture molecules onto the basesof the nanoscale wells, thereby immobilizing reactants to the bases ofthe nanoscale wells.

In further aspects, the present disclosure provides a method ofdelivering template nucleic acids to nanoscale wells that includes thesteps of: (a) providing an array of nanoscale wells; (b) providing anarray of chambers over the array of nanoscale wells, where the chambershave narrower openings than the nanoscale wells; (c) applying a solutionthat contains template nucleic acids to the array of chambers; (d)applying pressure or voltage to the solution to drive the templatenucleic acids into the chambers; (e) allowing the template nucleic acidsto passively diffuse from the chambers into the nanoscale wells, therebydelivering template nucleic acids to nanoscale wells. In someembodiments, the array of chambers includes a cathode, and the voltageapplied in step (d) is through an anode in the solution. In furtherembodiments, the array of chambers is designed such that the chambersalign with the nanoscale wells. In still further embodiments, thenanoscale wells further include polymerase enzymes. In yet furtherembodiments, the upper openings of the chambers are narrower than theopenings of the nanoscale wells.

In some aspects, the present disclosure provides a method of deliveringtemplate nucleic acids to nanoscale wells that includes the steps of:(a) providing an array of nanoscale wells, where a fluid-filled chamberis located above the array of nanoscale wells; (b) providing a loadingscreen to the top of the fluid-filled chamber where the loading screenincludes randomly placed holes; (c) applying a solution with templatenucleic acids to the loading screen; (d) applying pressure or voltage tothe solution to drive the template nucleic acids into the fluid-filledchamber through the holes of the loading screen; (e) allowing thetemplate nucleic acids to passively diffuse from the fluid-filledchamber into the nanoscale wells, thereby delivering template nucleicacids to nanoscale wells. In some embodiments, the nanoscale wells areabout 50 nm in diameter. In further embodiments, the randomly placedholes are about 30 to about 75 nm in diameter. In yet furtherembodiments, the template nucleic acids are from about 5 kb to about 20kb in length. In still further embodiments, the nanoscale wells furtherinclude polymerase enzymes.

In some aspects, the present disclosure provides method of deliveringpolymerase enzyme complexes to nanoscale wells that includes the stepsof:_(a) providing a surface that includes an array of nanoscalewells;_(b) coating the surface with a positively charged peptide to forma coated surface;_(c) applying a composition with polymerase enzymecomplexes to the coated surface such that at least a portion of thepolymerase enzyme complexes attach to the positively chargedpeptides;_(d) releasing the polymerase enzyme complexes from thepositively charged peptides or polypeptides to allow the polymeraseenzyme complexes to passively diffuse into the nanoscale wells, therebydelivering polymerase enzyme complexes to the nanoscale wells._In someembodiments, the releasing step includes applying a solution containinghigh salt to the coated surface. In some embodiments, the releasing stepincludes applying trypsin to the coated surface. In some embodiments,the releasing step includes applying a size exclusion resin to thecoated surface.

In further embodiments and in accordance with any of the above, thepositively charged peptide or polypeptide is a member selected from thegroup consisting of Tat, poly-lysine, poly-arginine, and histone.

In further embodiments and in accordance with any of the above, thepolymerase enzyme complexes include polymerase enzymes attached totemplate nucleic acid molecules. In still further embodiments, thetemplate nucleic acid molecules are further hybridized to a primer. Inyet further embodiments, the template nucleic acid molecules are atleast 5 kb long or are about 3 kb to about 20 kb in length.

In further embodiments and in accordance with any of the above, thedelivering of the polymerase enzyme complexes is accomplished about 4 toabout 100 times faster than seen with diffusion loading alone.

In further embodiments and in accordance with any of the above, thedelivering of the polymerase enzyme complexes is accomplished at least30, 40, 50, 60, 70 or 80 times faster than seen with diffusion loadingalone. In still further embodiments, the delivering of the polymeraseenzyme complexes is accomplished about 30 to about 150 times faster thanseen with diffusion loading alone. In yet further embodiments, thedelivering of the polymerase enzyme complexes is accomplished about 20to about 80 times faster than seen with diffusion loading alone.

In some aspects, the present disclosure provides a method of deliveringtemplate nucleic acids to nanoscale wells that includes the steps of:(a) providing an array of nanoscale wells; (b) providing at least onechannel over the array of nanoscale wells, wherein the at least onechannel comprises regions of greater and lesser confinement; (c)applying a solution containing template nucleic acids to the at leastone channel; (d) applying a driving force to the solution to move thetemplate nucleic acids through the channel over the nanoscale wells,where the regions of greater confinement serve as entropic barriers todelay or substantially prevent progress of the template nucleic acidsalong the channel; (e) allowing the template nucleic acids to passivelydiffuse from the at least one channel into the nanoscale wells, thusdelivering template nucleic acids to nanoscale wells. In furtherembodiments, the regions of greater confinement are located near thenanoscale wells, such that the entropic barriers posed by the regions ofgreater confinement serve to enrich the concentration of the templatenucleic acids over the nanoscale wells. In yet further embodiments, thedriving force includes an electrical potential or hydrodynamic pressure.

In further embodiments and in accordance with any of the above, theregions of greater and lesser confinement are alternately spaced alongthe channel.

In further embodiments and in accordance with any of the above, theregion of greater confinement has a depth of between about 5 nm andabout 500 nm, about 2 nm and about 100 nm, or about 30 nm and about 50nm.

In further embodiments and in accordance with any of the above, theapplying step (d) comprises a first phase and a second phase, where thefirst phase includes a high driving force to load the template nucleicacids into the channel and the second phase includes reducing thedriving force to collect the template nucleic acids at or near theentropic barriers.

In further embodiments and in accordance with any of the above, thetemplate nucleic acids are complexed with a polymerase enzyme inpolymerase enzyme complexes that are delivered to the nanoscale wells.In still further embodiments, the complexes further include a primerhybridized to the template nucleic acid. In yet further embodiments, themethod further includes the step of immobilizing the complexes to thebottom of the nanoscale wells, and in still further embodiments, thatimmobilizing includes an interaction between a first reaction moiety onthe bottom and a second reaction moiety on the polymerase enzyme ortemplate nucleic acid.

In further embodiments and in accordance with any of the above, the atleast one channel includes a number of channels equal to the number ofcolumns of nanoscale wells that are present in the array.

In further embodiments and in accordance with any of the above, themethod includes a step (f) analyzing the template nucleic acids locatedwithin the nanoscale wells.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic illustration of a loading method that utilizeshelix drive mechanisms.

FIG. 2 is a schematic illustration of a loading method that utilizesguidewire mechanisms.

FIG. 3 is a schematic illustration of embodiments of molecules that canbe used in loading methods that utilize winching or fishing mechanisms.

FIG. 4 is a schematic illustration of a loading method that utilizeswinching mechanisms and concatemers of template sequences.

FIG. 5 is a schematic illustration of an exemplary configuration of areaction site for use with a loading method that utilizeselectrodeposition mechanisms with capture molecules whose solubilitychanges with changes in pH.

FIG. 6A-FIG. 6C is a schematic illustration of an exemplaryconfiguration of a reaction site for use with a loading method thatutilizes electrophoretic mechanisms.

FIG. 7 is a schematic illustration of an exemplary configuration of areaction site for use with a loading method that utilizeselectrophoretic mechanisms.

FIG. 8 is a schematic illustration of an exemplary configuration of areaction site for use with a loading method that utilizeselectrophoretic mechanisms.

FIG. 9 is a schematic illustration of an exemplary configuration of areaction site for use with a loading method that utilizeselectrophoretic mechanisms.

FIG. 10 is a schematic illustration of an exemplary configuration of areaction site for use with a loading method that utilizeselectrophoretic mechanisms.

FIG. 11 is a schematic illustration of an exemplary configuration of areaction site for use with a loading method that utilizeselectrophoretic mechanisms.

FIG. 12 is a schematic illustration of a loading method that utilizesaffinity loading processes.

FIG. 13A-FIG. 13 C is a schematic illustration of a loading method thatutilizes guidewire mechanisms.

FIG. 14 is a schematic illustration of one embodiment of preparing atethering nucleic acid reagent for use in helix drive methods describedherein.

FIG. 15 is a schematic illustration of one embodiment of preparing atethering nucleic acid reagent for use in helix drive methods describedherein.

FIG. 16 a schematic illustration of one embodiment of preparing atethering nucleic acid reagent for use in helix drive methods describedherein.

FIG. 17 is a schematic illustration of a loading method that utilizesguidewire mechanisms.

FIG. 18A-B is a schematic illustration of exemplary configurations ofdevices for use in electrophoretic loading techniques, in side view.

FIG. 19 is a schematic illustration of an exemplary configuration of adevice for use in a loading technique utilizing entropic barriers.

FIG. 20 is a schematic illustration of an exemplary configuration of adevice for use in a loading technique utilizing entropic barriers.

FIG. 21 is a schematic illustration of an exemplary configuration of adevice for use in a loading technique utilizing entropic barriers.

FIG. 22 is a schematic illustration of an exemplary configuration of adevice for use in a loading technique utilizing entropic barriers.

DETAILED DESCRIPTION OF THE INVENTION

The practice of the present invention may employ, unless otherwiseindicated, conventional techniques and descriptions of organicchemistry, polymer technology, molecular biology (including recombinanttechniques), cell biology, biochemistry, and immunology, which arewithin the skill of the art. Such conventional techniques includepolymer array synthesis, hybridization, ligation, phage display, anddetection of hybridization using a label. Specific illustrations ofsuitable techniques can be had by reference to the examples hereinbelow. However, other equivalent conventional procedures can, of course,also be used. Such conventional techniques and descriptions can be foundin standard laboratory manuals such as Genome Analysis: A LaboratoryManual Series (Vols. I-IV), Using Antibodies: A Laboratory Manual,Cells: A Laboratory Manual, PCR Primer: A Laboratory Manual, andMolecular Cloning: A Laboratory Manual (all from Cold Spring HarborLaboratory Press), Stryer, L. (1995) Biochemistry (4th Ed.) Freeman, NewYork, Gait, “Oligonucleotide Synthesis: A Practical Approach”1984, IRLPress, London, Nelson and Cox (2000), Lehninger, Principles ofBiochemistry 3^(rd) Ed., W. H. Freeman Pub., New York, N.Y. and Berg etal. (2002) Biochemistry, 5^(th) Ed., W. H. Freeman Pub., New York, N.Y.,all of which are herein incorporated in their entirety by reference forall purposes.

Note that as used herein and in the appended claims, the singular forms“a,” “an,” and “the” include plural referents unless the context clearlydictates otherwise. Thus, for example, reference to “a polymerase”refers to one agent or mixtures of such agents, and reference to “themethod” includes reference to equivalent steps and methods known tothose skilled in the art, and so forth.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. All publications mentionedherein are incorporated herein by reference for the purpose ofdescribing and disclosing devices, compositions, formulations andmethodologies which are described in the publication and which might beused in connection with the presently described invention.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimit of that range and any other stated or intervening value in thatstated range is encompassed within the invention. The upper and lowerlimits of these smaller ranges may independently be included in thesmaller ranges is also encompassed within the invention, subject to anyspecifically excluded limit in the stated range. Where the stated rangeincludes one or both of the limits, ranges excluding either both ofthose included limits are also included in the invention.

In the following description, numerous specific details are set forth toprovide a more thorough understanding of the present invention. However,it will be apparent to one of skill in the art that the presentinvention may be practiced without one or more of these specificdetails. In other instances, well-known features and procedures wellknown to those skilled in the art have not been described in order toavoid obscuring the invention.

As used herein, the term “comprising” is intended to mean that thecompositions and methods include the recited elements, but not excludingothers. “Consisting essentially of” when used to define compositions andmethods, shall mean excluding other elements of any essentialsignificance to the composition or method. “Consisting of” shall meanexcluding more than trace elements of other ingredients for claimedcompositions and substantial method steps. Embodiments defined by eachof these transition terms are within the scope of this invention.Accordingly, it is intended that the methods and compositions caninclude additional steps and components (comprising) or alternativelyincluding steps and compositions of no significance (consistingessentially of) or alternatively, intending only the stated method stepsor compositions (consisting of).

All numerical designations, e.g., pH, temperature, time, concentration,and molecular weight, including ranges, are approximations which arevaried (+) or (−) by increments of 0.1. It is to be understood, althoughnot always explicitly stated that all numerical designations arepreceded by the term “about”. The term “about” also includes the exactvalue “X” in addition to minor increments of “X” such as “X+0.1” or“X−0.1.” It also is to be understood, although not always explicitlystated, that the reagents described herein are merely exemplary and thatequivalents of such are known in the art.

By “nucleic acid” or “oligonucleotide” or grammatical equivalents hereinmeans at least two nucleotides covalently linked together. A nucleicacid of the present invention will generally contain phosphodiesterbonds, although in some cases, nucleic acid analogs are included thatmay have alternate backbones, comprising, for example, phosphoramide,phosphorothioate, phosphorodithioate, and peptide nucleic acid backbonesand linkages. Other analog nucleic acids include those with positivebackbones; non-ionic backbones, and non-ribose backbones, includingthose described in U.S. Pat. Nos. 5,235,033 and 5,034,506. The templatenucleic acid may also have other modifications, such as the inclusion ofheteroatoms, the attachment of labels, such as dyes, or substitutionwith functional groups which will still allow for base pairing and forrecognition by the enzyme. The length of a nucleic acid can be indicatedin either nucleotides (measured on one strand of a single or doublestranded nucleic acid) or base pairs (measured on both strands of anucleic acid that is or that can be double stranded if hybridized to acomplementary strand); units of nucleotides and base pairs thus can beused interchangeably to refer to an identical length, as will be clearto one skilled in the art.

As used herein, a “substantially identical” nucleic acid is one that hasat least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to areference nucleic acid sequence. The length of comparison is preferablythe full length of the nucleic acid, but is generally at least 20nucleotides, 30 nucleotides, 40 nucleotides, 50 nucleotides, 75nucleotides, 100 nucleotides, 125 nucleotides, or more.

I. Overview

The active loading methods described herein enhance the loading of sites(also referred to herein as “reaction regions” and “array regions” and“nanoscale wells”) with an active mechanism that serves to overcomeentropic barriers that can be encountered by such molecules entering asite, particularly the entropic barriers that large molecules encounterduring loading into confined sites, for example when large templatenucleic acids (e.g., larger than 5 kb) are loaded into nanoscale wells.For ease of discussion, the loading methods described herein will oftenrefer to arrays of nanoscale wells. Such nanoscale wells can in certainexamples be zero mode waveguides (ZMWs), and in further examples, thoseZMWs may have biotionylated bases and passivated sides, which can be ofuse in the methods of loading described herein as well as in laterdownstream applications, such as sequencing reactions. As will beappreciated, any discussion herein referring to nanoscale wells and/orZMWs is applicable to any form of reaction sites and encompass all typesof surfaces, shapes and configurations of regions into which moleculesof interest can be loaded. These active loading methods provide theadvantages of reducing the amount of input molecules needed foreffective loading, reducing time required for loading, and/or reducingbackground noise for downstream reactions (such as sequencing reactions)by enriching for the molecules of interest, thus increasing performance(for example, for enriched loading of polymerases and polymerasecomplexes, downstream sequencing reactions show increased yield,readlength and accuracy).

For any of the methods described herein, the molecule of interest beingdelivered can be any molecule, including without limitation a templatenucleic acid, a polypeptide, an antibody, and a small molecule. Incertain examples, the molecule is a complex—for example, a polymeraseassociated with a template nucleic acid and optionally a primerhybridized to the template nucleic acid. For the ease of discussion,much of the discussion provided herein refers to molecules of interest,but as will be appreciated, any of the descriptions provided herein thatrefers to a molecule or molecules are equally applicable to a complex orcomplexes.

In some examples, the methods described herein utilize the ability ofself-complementary nucleic acids to form hairpin structures—this “helixdrive” mechanism allows any molecules associated with thoseself-complementary nucleic acids to be drawn along as the hybridizationbetween complementary regions occurs. In general, these mechanismsinvolve the use of a tethering nucleic acid that is located at areaction site. The tethering nucleic acid is double stranded, and atleast one of the strands includes self-complementary regions. One of thestrands (which contains self-complementary regions) includes at leastone capture moiety at one or both ends—that capture moiety can associatewith a molecule of interest. Once the molecule of interest is attachedto that strand through interaction with that capture moiety, the other(second) strand (the one without the capture moiety) is removed usingmethods known in the art, including for example enzymatic degradation,leaving the first strand attached to the molecule of interest. Theself-complementary regions of the first strand then hybridize to eachother, forming a hairpin—the formation of the more closed and compactconfiguration of that hairpin serves to draw the attached molecule ofinterest closer into the reaction site and thus delivers the molecule ofinterest to the reaction site. The molecule of interest may in someexamples then be immobilized to the reaction site for furtherprocessing.

In some examples, the methods described herein utilize “guidewires” toguide molecules of interest into the reaction site. In general, suchreaction sites include nanoscale wells such as ZMWs. In general, theguidewire comprises a linear molecule immobilized in a nanoscale well.The nanoscale well can be part of a surface comprising an array of suchnanoscale wells. The immobilized linear molecule has a length thatallows it to interact with molecules of interest that are distributed tothe surface and through that interaction capture at least one of thosemolecules. The immobilized linear molecule may be long enough toprotrude outside of the nanoscale well, or it may be of sufficientlength to reach partway up the height of the nanoscale well. The linearmolecule may capture the molecules of interest by any mechanisms knownin the art, including through electrostatic interactions, specificbinding moieties, or any other binding pairs. That capture increases theeffective concentration of the molecules of interest at the opening ofthe nanoscale well, resulting in an improved loading efficiency of thosemolecules into the nanoscale wells than is seen with passive diffusionalone. In further embodiments, the linear molecule is processed in orderto draw the linear molecule (and its captured molecule(s) of interest)into the nanoscale well. That processing may involve any mechanism thatserves to physically bring the end of the linear molecule that isattached to the molecule of interest into closer proximity to the pointat which the linear molecule is immobilized in the well (in specificexamples, to the base of the well). Once the molecule of interest isinside the well, it can in further embodiments be immobilized in thewell in turn. In specific embodiments, the processing does not involvethe use of a motor protein.

In some examples, the methods described herein utilize a “winching” or“fishing” mechanism to guide molecules of interest into the reactionsite. These methods include the use of a tethering nucleic acid moleculeimmobilized in the reaction site, which can be a nanoscale well. As inthe guidewire methods described herein, the tethering nucleic acidmolecule may be long enough to protrude outside of the nanoscale well,or it may be of sufficient length to reach partway up the height of thenanoscale well. In these winching methods, a plurality of templatenucleic acid monomers is distributed under conditions that allow for theligation of those template nucleic acid monomers to the tetheringnucleic acid molecules. Those ligated molecules can then be processed todraw the molecule into the nanoscale wells. The processing may includeany method that serves to physically bring the ligated molecules intothe wells—in certain examples, the processing includes the use of apolymerase enzymes within the nanoscale wells. The enzymes generate anascent strand from the ligated molecules and by that method draw theligated molecules into the wells. In further examples, prior to beingprocessed to draw the molecules into the well, further pluralities oftemplate nucleic acid monomers can be distributed to ligate additionalmonomers to the ends of the tethering nucleic acid. Any number ofmonomers can be so distributed, resulting in a ligated molecule thatcomprises a concatemer of the monomers distributed. The monomers makingup that concatemer may be identical to each other, or they may bedifferent. The concatemers may further include intervening linkermolecules to designate the end of one monomer and the start of the next.

In some examples, the methods described herein utilize a mechanism inwhich a capture molecule is delivered to a reaction site through the useof electrodeposition. Such mechanisms include the use of a capturemolecule that is water soluble and charged at one pH and water insolubleand uncharged at another pH. Thus, changing pH and applying a voltagedifferential can drive the capture molecule (and any associatedmolecules, such as template nucleic acids, polymerases, and/or complexescontaining both a template nucleic acid and a polymerase) to a reactionregion site. In further examples, these electrodeposition methods areused to immobilize reactants at the base of nanoscale wells. In suchexamples, the nanoscale wells may be part of an array. These arrays mayfurther include a solution layer above the wells as well as a conductinglayer that allows exposure of cathodes at or near the base of eachnanoscale well. Capture molecules are provided to the array, and thosecapture molecules will in certain examples have a pKa near neutral pH.In some examples, the capture molecules are water soluble in theirprotonated form and insoluble in their deprotonated form. Reactants canbe attached to the capture molecules, and a voltage applied through ananode in the solution layer to selectively deposit the capture moleculesonto the bases of the nanoscale wells, thus immobilizing the attachedreactants to the bases of the nanoscale wells. As will be appreciated,this configuration can be altered for capture molecules based on theirpKa, such that the voltage differential is produced by using a cathodein the solution layer and having the conducting layer that allowsexposure of anodes at or near the base of the nanoscale wells.

In some examples, the methods described herein utilize a mechanism inwhich template nucleic acids or similarly charged molecules aredelivered to a reaction site through the application of pressure orvoltage. In one example, the reaction sites are overlaid by an array ofchambers such that the chambers line up directly with the reactionsites. Voltage or pressure is used to drive molecules into the chambers.Then, because the reaction sites will typically have larger openingsthan the upper openings of the chambers, the molecules within thechambers are more likely to diffuse into the reaction site rather thanout of the chambers. In another example, a fluid-filled chamber islocated above the reaction sites, and a loading screen is provided tothe top of the fluid-filled chamber, wherein the loading screencomprises randomly placed holes. A solution containing template nucleicacids is applied to the loading screen and then pressure or voltage isapplied to the solution to drive the template nucleic acids into thefluid-filled chamber through the holes of the loading screen. Thetemplate nucleic acids then passively diffuse from the fluid-filledchamber into the nanoscale wells.

In some examples, the methods described herein utilize a mechanisminvolving affinity loading. In general, a surface containing reactionsites, such as nanoscale wells, is coated with a positively chargedpeptide. A composition containing molecules of interest containingnegative charges (such as polymerase enzyme complexes) is applied to thecoated surface such that at least a portion of the molecules attach tothe positively charged peptides. The molecules are then released fromthe positively charged surface to allow the polymerase enzyme complexesto passively diffuse into the nanoscale wells.

Any of the above described methods may be used alone or in anycombination with each other. In addition, any of the methods describedherein may be used in any combination with Super Poisson loading methodsand/or density loading methods known in the art and described forexample in U.S. Pat. No. 8,906,831, U.S. Ser. No. 15/078,915, filed Mar.23, 2016 and U.S. Ser. No. 62/257,152, filed Nov. 18, 2015, herebyincorporated by reference in their entirety for all purposes and inparticular for all teachings related to methods and compositions forloading reaction sites, such as nanoscale wells, with molecules ofinterest, such as polymerase enzyme-template complexes.

The above aspects and further exemplary embodiments are described infurther detail in the following discussion.

II. Helix Drive

In one aspect, the present disclosure provides methods of loadingmolecules onto sites by providing in the sites self-complementary singlestranded tethering nucleic acids that are initially held in anun-collapsed linear double-stranded state such that at least a portionof that tethering nucleic acid is outside the site. The tetheringnucleic acid will in general contain a capture moiety on one of thestrands that is able to interact with a molecule of interest, generallythrough a binding moiety associated with that molecule of interest. Thisinteraction between the tethering nucleic acid and the molecule ofinterest may be direct or indirect. The capture moiety on the tetheringnucleic acid may directly interact with a binding moiety on the moleculeof interest, or there may be an intervening entity through which thetethering nucleic acid associates with the molecule of interest. Forexample, as has been described herein, a molecule of interest inaccordance with any of the methods described herein may be part of acomplex. In an exemplary embodiment, the molecule of interest is atemplate nucleic acid that is complexed with a polymerase, and thepolymerase is what comprises the binding moiety that then interacts withthe capture moiety on the tethering nucleic acid to attach the complexto the tethering nucleic acid.

After attachment of the molecule to the tethering nucleic acid, thestrand of the tethering nucleic acid that is not attached to themolecule (e.g., the strand that does not contain the capture moiety) isdegraded, causing the remaining strand, which is self-complementary, tocollapse into a large hairpin in which the ends are brought together.That movement of collapsing into the hairpin configuration serves tobring the tethering nucleic acid and its attached molecule into thereaction site.

FIG. 1 provides an exemplary illustration of the helix drive process. Areaction site 101 contains immobilization regions 102. In step (103), atethering nucleic acid 104 is immobilized to the immobilization regions,generally via only one of the two strands. That same strand contains acapture moiety. Molecules of interest are distributed (105) such that atleast one molecule of interest (106) interacts with that capture moietyto attach to that strand. The other strand of the tethering nucleic acidis removed (107), leaving the single tethering nucleic acid strand (108)attached to the molecule of interest (106). The single tethering nucleicacid strand contains self-complementary regions that cause the tether tofold into a hairpin shape (109), thus bringing the attached moleculeinto the interior of the reaction site. In further step(s) 110, themolecule of interest can be immobilized to the base of the reactionsite, including in a further exemplary embodiment to an immobilizationregion 102. In further embodiments, the remaining tethering nucleic acidstrand can be removed, leaving the molecule of interest in the reactionsite. The two strands of the tethering nucleic acid are optionallydifferent molecules as shown in FIG. 1 , or can be part of the samemolecule (e.g., a large hairpin or a circular nucleic acid). Althoughdiscussed for simplicity in terms of a single tethering nucleic acid perwell or site, it will be evident that the well or site optionallyincludes multiple tethering nucleic acids.

In certain embodiments, the reaction site is a nanoscale well, and themolecule of interest is a complex containing a polymerase enzymecomplexed with a template nucleic acid with a primer optionally alsohybridized to the template nucleic acid. In embodiments in which themolecule is a template nucleic acid or a complex containing templatenucleic acid, the template nucleic acid may comprise DNA, RNA, or acombination of both.

In certain embodiments the capture of the molecule of interest involvesan interaction between a capture moiety on the tethering nucleic acidand a binding moiety on the molecule of interest. As will beappreciated, in embodiments involving complexes, the binding moiety maybe located on any component of the complex—for example, for complexescontaining a polymerase enzyme and a template nucleic acid, the bindingmoiety may be on the template nucleic acid or on the polymerase enzyme.The capture moiety on the tethering nucleic acid and the binding moietyon the molecule of interest may comprise any pair that can react witheach other, including without limitation antigen-antibody binding pairs,receptor-ligand binding pairs, aptamer-epitope binding pairs,GST/glutathione pairs, nucleic acid hybridization pairs, and the like.In specific embodiments, the capture moiety and the binding moietycomprise biotin and streptavidin respectively (or vice versa). It willbe evident that avidin, traptavidin, neutravidin, or other knownbiotin-binding moieties can be substituted for streptavidin whereverstreptavidin is specified herein.

In certain embodiments, the tethering nucleic acid contains capturemoieties on both ends of the strand that is not degraded. That capturemoiety may be any member of the pairs described above. In specificembodiments, the capture moiety is a biotin, and the binding moiety onthe molecule of interest is streptavidin. In further embodiments, thereaction site also contains binding moieties, and the tethering nucleicacid is immobilized to the reaction site through an interaction betweenthe capture moiety on one end and the binding moiety on the reactionsite. In some embodiments, the capture moieties on both ends of thetethering nucleic acid are identical. In some embodiments, the capturemoieties on the two ends of the tethering nucleic acid are differentfrom each other. In such embodiments, the tethering nucleic acid can bedesigned to have a polarity with respect to the reaction site, such thatthe capture moiety designed to pair with the molecule of interest isleft free while the other end of the tethering nucleic acid isimmobilized to the reaction site.

In some embodiments and in accordance with any of the above, thetethering nucleic acid is immobilized to a surface, generally a surfaceof a reaction site, including for example the base of a nanoscale well.In further embodiments, the immobilization to the surface is through anymeans of attachment, including the binding pairs discussed above or anyother noncovalent or covalent attachment, electrostatic interaction,attachment through a linker or some other intervening molecule, or anyother method by which the tethering nucleic acid molecule is connectedto the reaction site.

In certain aspects, the collapsing of the tethering nucleic acid strandinto a hairpin serves to bring the attached molecule of interest and/orcomplex close enough to the reaction site to allow the complex to becomeimmobilized to the reaction site through any number of interactions,including covalent attachment, electrostatic interaction, attachmentthrough a linker or some other intervening molecule, or any other methodby which the molecule of interest is connected to the reaction site. Incertain embodiments, the complex is immobilized to a reaction site usingpeptide linker systems, including for example SpyTag/SpyCatcher systemssuch as those described in for example Fairhead et al., (J. Am. Chem.Soc., 2014, 136: 12355-12363), which is hereby incorporated in itsentirety for all purposes including all teachings related to assemblingcomplexes utilizing SpyTag and SpyCatcher components. In an exemplaryembodiment, streptavidin tetramers are used in which one of the foursubunits bears the SpyTag and the SpyCatcher component is on thepolymerase, although the reverse configuration can also be used. Similarconstructs are further described in detail in Fairhead et al. Forexample, the base of a nanoscale well can bear biotin groups to which aSpyTagged streptavidin is bound. The nucleic acid tether can then beimmobilized to the base of the well by binding to a biotin capturemoiety on one end of the tether. A SpyCatcher-polymerase/templatecomplex is captured by the other end of the tether and brought into thewell, where the SpyCatcher fusion polymerase can react with theSpyTagged streptavidin, immobilizing the polymerase/template complex. Inother embodiments, a biotinylated polymerase can be immobilized viastreptavidin binding to a biotinylated site, e.g., the base of ananoscale well.

In further embodiments, the tethering nucleic acid contains multiplecapture moieties, thus increasing the points at which molecule(s) ofinterest can be captured and/or points at which the tethering nucleicacid can be immobilized to the reaction site. In some embodiments, thetethering nucleic acid includes a scaffold comprising multiple capturemoieties. In further embodiments, the scaffold is a star-shapedscaffold. Generally, the core of the scaffold is a polymer, although anymolecule or composition capable of attachment to multiple functionalmoieties may be used as the core. In certain non-limiting examples, thecore of the scaffold is a multi-arm polyethylene glycol molecule or aDNA construct. In still further examples, the core of the scaffold isattached to multiple arms containing capture moieties that are able tointeract with binding moieties on the molecule of interest. In someembodiment these arms comprise oligonucleotides that are about 25 toabout 250, about 50 to about 100, about 75 to about 200 bp in length.Scaffolds of use with any of the tethering molecules described hereinare described for example in U.S. Ser. No. 15/078,915, filed Mar. 23,2016, which is hereby incorporated by reference in its entirety for allpurposes and in particular for all teachings related to scaffoldconstructs and methods for binding molecules to same.

As discussed above, one part of the helix drive process is that thestrand of the tethering nucleic acid that is not bound to the moleculeof interest is degraded to allow the bound strand to collapse into ahairpin due to its self-complementary regions. That degradation of theunbound “second” strand can be accomplished by any method known in theart, including enzymatic degradation. The degradation method used willbe determined by the design of the tethering nucleic acid, particularlythe second strand. In general, the first strand bound to the molecule ofinterest is protected from degradation in some way and the second strandis designed to be sensitive. For example, if the first strand isresistant to exonuclease, and the second is sensitive (or is madesensitive at some point through treatment with a nickase, etc.),incubation with exonuclease would degrade the sensitive strand andgenerate the above-described hairpin. In further embodiments, the secondstrand comprises RNA and the first strand comprises DNA— the use ofRNAse would then degrade the second strand while the first strandremains intact. In still further embodiments, the second strand containsdU (deoxyuridine)—in such embodiments, application of UDG (uracil-DNAglycosylase) followed by endonuclease VIII would result in selectivedegradation of the second strand. In other embodiments, the secondstrand contains deoxyinosine; in such embodiments, application ofendonuclease V would result in selective degradation of the secondstrand.

In further embodiments and in accordance with any of the above, themolecule of interest that is captured by the tethering nucleic acid is amember selected from the group consisting of: a template nucleic acid, apolypeptide, an antibody, and a small molecule. In still furtherembodiments, the molecule is part of a complex. In yet furtherembodiments, the complex includes a template nucleic acid complexed witha polymerase enzyme and may optionally include a primer hybridized tothe template nucleic acid.

In certain embodiments, the tethering nucleic acid molecule is ofsufficient length to protrude outside of the reaction site. Inembodiments in which the reaction site comprises a nanoscale well, thiswould mean that the tether is at or above the opening of the well. Inother embodiments, the tethering nucleic acid molecule may not protrudeoutside of the reaction site, but nevertheless has sufficient length tointeract with molecules that are in proximity to the reaction site. Infurther embodiments, the tethering nucleic acid is at least or about500, 750, 1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500,6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, 10000basepairs/nucleotides in length.

Any of the above-described helix drive loading methods may also be usedfor reaction sites that are nanopores. In such embodiments, thetethering nucleic acids are generally located proximal to the nanoporerather than directly inside the nanopore. Any of the above describedmethods for the helix drive process are applicable to use with reactionsites comprising nanopores.

In yet further embodiments, any of the helix drive loading methodsdescribed herein may be combined with other loading methods, includingSuper Poisson loading and density loading methods known in the art anddescribed for example in U.S. Pat. No. 8,906,831, U.S. Ser. No.15/078,915, filed Mar. 23, 2016 and U.S. Ser. No. 62/257,152, filed Nov.18, 2015, hereby incorporated by reference in their entirety for allpurposes.

III. Guidewire

In one aspect, the present disclosure provides methods for activeloading of molecules, including without limitation template nucleicacids and complexes that include template nucleic acids, into a reactionsite that includes a “guidewire” to guide the desired molecule into thereaction site. In general, such reaction sites include nanoscale wellssuch as ZMWs.

FIG. 2 provides a schematic illustration of an example of a method ofloading utilizing a guidewire. In this exemplary aspect, the guidewirecomprises a linear molecule (201) immobilized in a nanoscale well (202).The nanoscale well can be part of a surface comprising an array of suchnanoscale wells. The immobilized linear molecule has a length thatallows it to interact with molecules of interest (205) that aredistributed to (e.g., disposed on the surface or in a solution disposedon the surface) (204) and capture at least one of those molecules (206).The immobilized linear molecule may be long enough to protrude outsideof the nanoscale well, or it may be of sufficient length to reachpartway up the height of the nanoscale well, e.g., when one end isimmobilized at the base of the well (203). In further embodiments, thelinear molecule has a length that is at least about 2×, 3×, 4×, 5×, 10×,15×, 20×, 25×, 30×, 40×, 50× the height of the nanoscale well. Infurther embodiments, the linear molecule has a length that is at leastabout 3×, 4×, 5×, 10×, 15×, 20×, 25×, 30×, 40×, 50× the cross-sectionaldiameter of the linear molecule. The linear molecule may capture themolecules of interest by any mechanisms known in the art, includingthrough electrostatic interactions, specific binding moieties, or anyother binding pairs, including without limitation biotin-streptavidinbinding pairs, antigen-antibody binding pairs, receptor-ligand bindingpairs, aptamer-epitope binding pairs, GST/glutathione pairs, nucleicacid hybridization pairs, and the like. In embodiments in which themolecule of interest includes a template nucleic acid, the templatenucleic acid may comprise a 5′ overhang and the guidewires can comprisetethered nucleic acid molecules that comprise a 3′ overhang, such thatthe capture of the template nucleic acids is by hybridization ofmatching overhangs between the tethered nucleic acid molecules and thetemplate nucleic acids. In another example, the tethering nucleic acidis single-stranded or includes a single-stranded portion that hybridizesto a single-stranded portion of the template, e.g., to a hairpin loop ina SMRTbell™ or other primarily double-stranded molecule. In otherembodiments, the capture of the molecule of interest involves aninteraction between a capture moiety on the guidewire and a bindingmoiety on the molecule of interest. As will be appreciated, inembodiments involving complexes, the binding moiety may be located onany component of the complex—for example, for complexes containing apolymerase enzyme and a template nucleic acid, the binding moiety may beon the template nucleic acid or on the polymerase enzyme.

Whatever mechanism of capture is used, the result is an increase in theeffective concentration of the molecules of interest at or near theopening of the nanoscale well, resulting in an improved loadingefficiency of those molecules into the nanoscale wells than is seen withpassive diffusion alone. In further embodiments, the linear molecule isprocessed in order to draw the linear molecule (and its capturedmolecule(s) of interest) into the nanoscale well. That processing mayinvolve any mechanism that serves to physically bring the end of thelinear molecule that is attached to the molecule of interest into closerproximity to the point at which the linear molecule is immobilized inthe well (in specific embodiments, at the base of the well). Once themolecule of interest is inside the well, it can in further embodimentsbe immobilized in the well in turn, e.g., at the base of the well. Inspecific embodiments, the processing does not involve the use of a motorprotein.

In specific aspects, the guidewire comprises a tethering nucleic acidmolecule immobilized in a nanoscale well, generally at the base of thewell. In further aspects, each nanoscale well will have multipleguidewires/tethering nucleic acid molecules. The tethering nucleic acidmay include without limitation a single stranded nucleic acid, a doublestranded nucleic acid, or a partially double stranded and a partiallysingle stranded nucleic acid. In specific embodiments, the tetheringnucleic acid comprises DNA. In further specific embodiments, thetethering nucleic acid is a circular construct, such as those describedin, e.g., U.S. Pat. No. 7,315,019 and U.S. patent application Ser. No.12/220,674, filed Jul. 25, 2008, and alternate functional circularconstructs as described in US Pat. App. Pub. No. 20090298075, the fulldisclosures of each of which are incorporated herein by reference intheir entirety for all purposes and in particular for all teachingsrelated to nucleic acid constructs. Briefly, such alternate constructsinclude template sequences that possess a central double strandedportion that is linked at each end by an appropriate linkingoligonucleotide, such as a hairpin loop segment. In further embodiments,there is a cleavable linker between the guidewire and the point at whichit is immobilized to the reaction site surface. In yet furtherembodiments, the guidewire methods described herein include a step ofapplying a composition to cleave the cleavable linker the guidewiresonce the molecules of interest have been successfully loaded into thereaction site and optionally immobilized. In specific embodiments, thecleavable linker includes a protease recognition site, and the guidewireis released by application of a protease to the reaction site. Infurther embodiments, the cleavable linkage may be part of the guidewireor a moiety on the guidewire. In one non-limiting example, the guidewireis immobilized to the reaction site through a streptavidin molecule, andthe cleavage site is located within the streptavidin molecule itself

As discussed above, in some embodiments, the tethering nucleic acid islong enough to protrude outside the well, whereas in some embodimentsthe tethering nucleic acid is shorter than the height of the nanoscalewell. In embodiments involving an array of nanoscale wells, all thetethering nucleic acids may protrude outside the well, all the tetheringnucleic acids may be shorter than the height of the nanoscale well, orthere may be a mixture of protruding and shorter tethering nucleicacids.

Because they are generally small (around 1000 basepairs) and can beprovided at relatively high concentration, the tethering nucleic acidscan be loaded efficiently into the reaction sites. In certainembodiments, the tethering nucleic acids are from about 750 to about4000 bp/nt in length. In further embodiments, the tethering nucleicacids are 1000-1500, 1000-2000, 1250-3500, 1500-3000, 1750-2000,1000-5000 bp/nt in length. In still further embodiments, the tetheringnucleic acids are at least or about 500, 750, 1000, 1500, 2000, 2500,3000, 3500, 4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500,9000, 9500, 10000 bp/nt in length.

In certain embodiments, the tethering nucleic acid molecules areprocessed after capture of the molecules of interest to further draw thetethering nucleic acids and the captured molecules into the nanoscalewells. In an exemplary embodiment, the tethering nucleic acid moleculeis processed by a polymerase enzyme (i.e., is employed as a template),and the act of the polymerase generating a nascent strand serves to drawthe tethering nucleic acid molecule and its captured molecule into thenanoscale well where the polymerase is immobilized. In furtherembodiments, the processing proceeds until the captured molecules arethemselves immobilized in the nanoscale wells using methods known in theart and described herein. In specific embodiments, the capturedmolecules are immobilized through an interaction between a moiety on thecaptured molecules and a moiety in the nanoscale wells.

As discussed herein, the molecules of interest can include any moleculeincluding without limitation a template nucleic acid, a polypeptide, anantibody, and a small molecule, as well as complexes involving one ormore of such molecules. In an exemplary embodiment, the molecules ofinterest comprise template nucleic acids. In a further embodiment, thetemplate nucleic acids are complexed with a polymerase and optionallyare also hybridized to a primer. In certain embodiments, these complexesare maintained in an inactive or locked state. In embodiments in whichthe tethering nucleic acid is drawn into the nanoscale well by theprocessing action of a polymerase that is immobilized at the base of thewell, maintaining the complex of interest in a locked state allows thepolymerase at the base of the well to proceed without allowing thepolymerase in the complex to begin its own reaction until needed (i.e.,until the complex is brought into the nanoscale well). This locked stateallows the complex to be loaded into the nanoscale well before it isactivated for downstream reactions, particularly sequencingreactions—thus, the guidewire methods allow the surface to be properlyloaded with the complexes prior to starting the reactions that allowgeneration of data such as sequencing data. In further embodiments, thelocked state may be maintained by binding a complex including a modifiedrecombinant polymerase with a nonhydrolyzable hexaphosphate analog(unlike nonhydrolyzable triphosphates, the hexaphosphate analog willgenerally not bind well to wildtype polymerase enzymes, such as thosethat would in further embodiments be used to process the tetheringnucleic acid to bring it and its attached complex into the reactionsite/nanoscale well; suitable modified polymerases are describedhereinbelow).

A specific embodiment of the guidewire method is illustrated in FIGS.13A-C. The first step, shown in FIG. 13A, involves adding a heavilybiotinylated duplex to a chip coated with spytag-streptavidin. Althoughone copy is shown, generally multiple biotinylated DNA molecules wouldbe immobilized in a ZMW well. The second step shown in FIG. 13B involvesbinding a polymerase/nucleic acid complex containing aspycatcher/biotin-tagged polymerase fusion to the guidewire molecule,via streptavidin that binds to biotins both on the guidewire and on thespycatcher-polymerase fusion. As shown in FIG. 13C, the complex is nowbound to the guidewire. Next spontaneous formation of thespycatcher-spytag bond immobilizes the polymerase and its bound templatenucleic acid at the base of the ZMW, inside the illuminated volume.

In certain embodiments, the guidewire molecule is not a nucleic acidmolecule. As will be appreciated, any molecule or composition that isable to capture a molecule of interest and guide it into the reactionsite could be used in these guidewire mechanisms. In an exemplaryembodiment, the guidewire/tether involves M13 phage particles. Theseparticles are stiff rods that can be placed in a reaction site and havelength to reach out of the reaction site (or at least to a height thatallows interaction with distributed molecules of interest). Any M13phage particles known in the art can be used in accordance with themethods described herein. In general, these particles are engineered tohave affinity for the molecule of interest. For example, for capture ofa template nucleic acid, M13 particles having a cationic peptide (e.g.,tetraArg) fused to the major coat protein pVIII can be employed. Suchparticles have been described, e.g., in Liu et al., Adv. Mater. 2009,21: 1001-1005, which is hereby incorporated in its entirety for allpurposes and in particular for all teachings related to M13 phageparticles. In some embodiments, the pill proteins at the tail areengineered to have streptavidin affinity, allowing immobilization of theM13 particles at a properly functionalized reaction site. In specificembodiments, the reaction site may be a nanoscale well in which the basehas been functionalized with biotin, to which streptavidin can be bound.An M13 particle having a peptide with affinity for SA on pill has beendescribed (see Nam et al. “Genetically Driven Assembly of NanoringsBased on the M13 Virus” Nano Letters, 2004, 4 (1), pp 23-27, which ishereby incorporated by reference in its entirety for all purposes). Thusin one exemplary embodiment for capture of a template/polymerasecomplex, an M13 particle having a cationic peptide, including withoutlimitation tetraArg, fused to pVIII and a streptavidin binding peptidefused to pill is immobilized on the biotinylated, streptavidin coatedbase of a nanoscale well. The molecule of interest, generally apolymerase/template nucleic acid complex, is then added and captured bythe particle. In another exemplary embodiment, M13 particles selectedfor affinity to a particular surface material, e.g., the silica bottomof a ZMW, and also bearing RRRR on pVIII are employed for capture of thetemplate/polymerase complex. See also Seker et al., Molecules, 2011, 16:1426-1461. In another exemplary embodiment, starting again with ananoscale well functionalized at the base with biotin, streptavidinfused to a protein is bound to the biotin. The nanoscale well is thenwashed with M13 containing RRRR on the major coat protein pVIII and apeptide with affinity for the streptavidin-bound protein on pill, so theM13 becomes attached to the protein bound to the bottom of the well. Thetemplate/polymerase complex can then be added and will be captured tothe RRRR sequence.

IV. Winching

In one aspect, the present disclosure provides methods for activeloading of molecules, including without limitation template nucleicacids and complexes that include template nucleic acids, into reactionsites by utilizing “winching” or “fishing” lines that are used tocapture the molecules of interest into the reaction sites. In general,such reaction sites can include without limitation nanoscale wells. Thewinching or fishing lines can include any type of molecule or polymerthat can serve as a tether that can ligate to one or more molecules ofinterest and then undergo a processing step that draws the tether andits captured molecule(s) further into the interior of the reaction site.The winching or fishing lines may further be of a length to protrudeoutside of the reaction site, although in some embodiments thewinching/fishing lines have a length sufficient to interact withdistributed molecules of interest, but are not necessarily long enoughto protrude outside the reaction site.

In an exemplary embodiment, these methods include the use of a tetheringnucleic acid molecule immobilized in a nanoscale well. As in theguidewire methods described herein, the tethering nucleic acid moleculein the winching methods may be long enough to protrude outside of thenanoscale well, or it may be of a length to reach partway up the heightof the nanoscale well. In specific embodiments, these methods areconducted using a surface comprising a plurality of nanoscale wellscontaining the immobilized tethering nucleic acid molecule. A pluralityof template nucleic acid monomers is distributed under conditions thatallow for the ligation of those template nucleic acid monomers to thetethering nucleic acid molecules. Those ligated molecules can then beprocessed to draw the molecule into the nanoscale wells. The processingmay include any method that serves to physically bring the ligatedmolecules into the wells—in certain examples, the processing includesthe use of polymerase enzymes within the nanoscale wells. The enzymesgenerate a nascent strand from the ligated molecules and by that methoddraw the ligated molecules into the wells.

In further examples, prior to being processed to draw the molecules intothe well, further pluralities of template nucleic acid monomers aredistributed to ligate additional monomers to the ends of the tetheringnucleic acid. Any number of monomers can be so distributed, resulting ina ligated molecule that comprises a concatemer of the monomersdistributed. The monomers making up that concatemer may be identical toeach other, or they may be different. The concatemers may furtherinclude intervening linker molecules to designate the end of one monomerand the start of the next. These linker molecules may includeoligonucleotide sequences, and in further embodiments theseoligonucleotide sequences are of known sequence and can in still furtherembodiments serve as barcodes for the adjacent template nucleic acidmonomers. Increasing the number of monomers and intervening linkers canimprove genomic coverage by providing more independent, long subreads indownstream sequencing reactions. The linker molecules can be distributedand then ligated to the ends of each concatemer in intervening cyclesbetween distribution of template nucleic acid monomers. More typically,multiple template monomers and intervening connectors are distributed tothe surface and ligated in a single reaction step. Control over theligation to ensure that the linkers only bind to the end of the templatenucleic acid monomers rather than to each other can be established bydesigning overhangs of the linkers such that they are only able toligate to the monomers but not to each other. See, e.g., the exemplary200 base pair linker in FIG. 3 , whose overhangs are complementary tothe overhangs on the template monomer but not to the overhang on thewinching tether. Similarly, the overhangs on the monomers can be choseto ensure that they bind to the winch and linkers rather than to eachother. Overhangs of 1, 2, 3, 4, 5, 6, or more bases are optionallyprovided.

As will be appreciated, the concatemers described above can be of anylength, as the ability to load them into the reaction sites issignificantly improved by the use of the winching tethering nucleicacids. The concatemers may in further embodiments be about 3000-150,000nucleotides in length. In still further embodiments, the concatemers areabout 4000-18000, 5000-16000, 6000-14000, 8000-12000, 10000-11000,10000-50000, 20000-60000, 30000-70000, 40000-80000, 50000-90000,10000-100000, 20000-80000, 30000-60000, 80000-200000, 90000-180000,100000-160000, 110000-140000 nucleotides in length. In furtherembodiments, the concatemers are at least about 15,000; 20,000; 25,000;30,000; 40,000; 50,000; 60,000; 70,000; 80,000; 90,000; 100,000;120,000; 130,000; 140,000; 150,000 nucleotides in length.

In further embodiments and in accordance with any of the above, thetethering nucleic acid molecules are at least about 1000 to about 5000nucleotides in length. In still further embodiments, the tetheringnucleic acid molecules are about 1000-10000, 1500-9000, 2000-8000,2500-7000, 3000-6000, 3500-5000, 4000-4500 bp (the equivalents for anynon-nucleic acid winching molecules) in length. In yet furtherembodiments, the tethering nucleic acid molecules are about 500, 750,1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500, 6000, 6500,7000, 7500, 8000, 8500, 9000, 9500, 10000 bp (or the equivalent thereoffor non-nucleic acid winching molecules) in length.

As is described in further detail herein, the template nucleic acidmonomers may be of any structure and may comprise without limitationDNA, RNA, or a mixture of DNA and RNA. In certain aspects, any of thewinching mechanisms described above result in a ligated sequencingtemplate that comprises one or more template nucleic acid monomersligated in series to a winching molecule such as a tethering nucleicacid. In some embodiments, the ligated sequencing templates in theirfinal form before the processing that draws the ligated molecule intothe reaction site comprise a hairpin loop at one or both ends of theligated sequencing template. Such hairpin loops can provide a way forany subsequent sequencing reactions to provide redundant sequencinginformation by allowing the sequencing reaction to proceed along bothstrands of the double stranded portion of the ligated sequencingtemplate, e.g., when added to the terminal template monomer.

As discussed above, the winching molecules are generally immobilizedwithin the reaction site. In embodiments in which the reaction sites arenanoscale wells, the immobilization may be at or near the base of thenanoscale wells. In further embodiments, the winching molecules aretethering nucleic acid molecules that are immobilized throughassociation with a polymerase enzyme that is itself immobilized on thereaction site (such as at or near the base of a nanoscale well), e.g.,through interaction of a biotinylated polymerase with streptavidin thatis in turn bound to a biotinylated surface.

In embodiments in which a polymerase is used to process the winchingmolecule to bring it and the captured molecule/complex of interest intothe reaction site, the polymerase may be maintained in an inactive stateuntil the molecule/complex is ready to be brought into the reactionsite. This provides control over the system such that the winchingmolecule is not brought into the site until all ligation steps andcapture of the molecule of interest onto the winch is complete. Anymethod known for maintaining polymerases in an inactive state, includingthe use of analogs that cannot be processed by the polymerases (e.g.,non-hydrolyzable analogs) can be used. In other embodiments,polymerization rate can be slowed by employing a low concentration ofnucleotides or analogs. In addition, the winch can be locked into placeon the polymerase, for example with chemical cross-links. For example, abifunctional cross-linker can be reacted with residues in the polymeraseon each side of the bound winching molecule (which will in thisembodiment generally be a tethering nucleic acid), topologicallyencircling it to stabilize the polymerase/nucleic acid complex. See,e.g., U.S. Pat. No. 7,745,116 and US patent application publication2015/0086994, each of which is incorporated herein by reference in itsentirety for all purposes, and in particular for all teachings relatedto locking enzymes. Cysteine residues can be introduced into thepolymerase at suitable positions for cross-link formation. For example,a recombinant ϕ29 polymerase can include, e.g., A83C and E420Csubstitutions, D84C and E418C substitutions, V19C and N409Csubstitutions, and/or N409C and V568C substitutions. (See, e.g., USpatent application publication 2014/0094375, incorporated herein byreference in its entirety for all purposes, for the sequence ofwild-type ϕ29 polymerase.) Existing solvent accessible cysteine residuescan be mutated to ensure that the cross-link is formed between thedesired pair of residues; thus, a suitable recombinant ϕ29 polymerasecan also include one or more substitutions such as, e.g., C106S and/orC448V. Suitable bifunctional linkers are known in the art, for example,a bismaleimide linker, e.g., a bismaleimide-PEG linker, e.g.,1,11-bismaleimido-triethyleneglycol (BM(PEG)₃). Other couplingchemistries that can be employed include, e.g., thiol reactive reagentsand disulfide containing reagents, e.g., haloacetyl crosslinkers (e.g.,linkers including two iodoacetyl/iodoacetamide or bromoacetyl groups)and linkers with two pyridyl disulfide groups. The body of the linkercan include, e.g., PEG (polyethylene glycol), an oligopeptide (e.g.,polyglycine), or the like. Optimal linker length can be chosen based onthe distance between the two residues to be cross-linked, e.g., in acrystal structure or other model of the polymerase. The linker istypically reacted with the polymerase after binding of the template (orprimer/template); suitable reaction conditions for various linkerchemistries are known in the art. Noncovalent linkers can also beemployed. Such topological encirclement of the nucleic acid bypolymerase can be particularly effective for circular nucleic acidmolecules (including, e.g., simple circles and SMRTbells™ as describedin, e.g., U.S. Pat. No. 8,153,375 “Compositions and Methods for NucleicAcid Sequencing” and Travers et al. (2010) Nucl. Acids Res. 38(15):e159,each of which is incorporated herein by reference in its entirety forall purposes).

The winching methods described herein may in further embodiments benefitfrom use of polymerases that lack exonuclease activity to avoiddegradation of the primer. Accordingly, polymerases for use in the abovetechniques optionally include one or more mutations (e.g.,substitutions, insertions, and/or deletions) relative to the parentalpolymerase that reduce or eliminate endogenous exonuclease activity. Forexample, relative to wild-type ϕ29 DNA polymerase, one or more ofpositions N62, D12, E14, T15, H61, D66, D169, K143, Y148, and H149 isoptionally mutated to reduce exonuclease activity in a recombinant ϕ29polymerase. Exemplary mutations that can reduce exonuclease activity ina recombinant ϕ29 polymerase include, e.g., N62D, N62H, D12A, T151,E14I, E14A, D66A, K143D, D145A and D169A substitutions, as well asaddition of an exogenous feature at the C-terminus (e.g., apolyhistidine tag). See, e.g., US patent application publication2014/0094375, incorporated herein by reference in its entirety for allpurposes, for the sequence of wild-type ϕ29 polymerase. In furtherembodiments, the primer can incorporate one or more phosphorothioate orsimilar linkages to resist exonuclease activity of the polymerase.

Suitable ligases (e.g., T4 ligase or a single-stranded DNA damage repairligase) are well known in the art and are commercially available.Appropriate reaction conditions are similarly known. Addition of a“crowding” agent such as polyethylene glycol and/or use of an increasedconcentration of ligase can be helpful in some instances. In someembodiments, loading of the tether, provision of the template monomers,and/or ligation can benefit from density loading techniques such asthose described in U.S. Ser. No. 62/257,152, filed Nov. 18, 2015, herebyincorporated by reference in its entirety for all purposes. In certainembodiments, rather than ligation, recombinase or transposase techniques(e.g., cre-lox recombination) known in the art can be used to createconcatemers used in the methods described herein.

V. Electro deposition

In some examples, the methods described herein utilize a mechanism inwhich a capture molecule is delivered to a reaction site through the useof electrodeposition. Such mechanisms include the use of a capturemolecule that is water soluble and charged at one pH and water insolubleand uncharged at another pH. Thus, changing pH, for example, by applyinga voltage differential and taking advantage of the pH change atelectrodes in solution, can deposit and immobilize the capture molecule(and any associated molecules, such as template nucleic acids,polymerases, and/or complexes containing both a template nucleic acidand a polymerase) to a reaction region site. In further examples, theseelectrodeposition methods are used to immobilize reactants at the baseof nanoscale wells. In such examples, the nanoscale wells may be part ofan array. These arrays may further include a solution layer above thewells as well as a conducting layer that allows exposure of cathodes ator near the base of each nanoscale well. Capture molecules are providedto the array, and those capture molecules will in certain examples havea pKa near neutral pH, e.g., a pKa between 6.0 and 8.0. In someexamples, the capture molecules are water soluble in their protonated,charged form and insoluble in their deprotonated, uncharged form.Exemplary such capture molecules include polycations such as chitosan,polyimidazole, and polyhistidine. Reactants can be attached to thecapture molecules, and a voltage applied through an anode in thesolution layer to selectively deposit the capture molecules onto thebases of the nanoscale wells, thus immobilizing the attached reactantsto the bases of the nanoscale wells. As will be appreciated, thisconfiguration can be altered for capture molecules based on their pKa,such that the voltage differential is produced by using a cathode in thesolution layer and having the conducting layer that allows exposure ofanodes at or near the base of the nanoscale wells, e.g., forelectrodeposition of capture molecules that are water soluble in theirdeprotonated, charged form and insoluble in their protonated, unchargedform, e.g., polyanions such as alginate.

One embodiment of the invention is illustrated in FIG. 5 . As shown, thedevice includes an insulating layer, a conducting layer, and atransparent insulator. A nanoscale well is provided that reaches throughthe insulating and conducting layer to have a base within thetransparent insulator. The conducting layer is situated to allowexposure of cathodes at or near the base of the nanoscale well. Capturemolecules 501 are provided to a solution layer above the nanoscale well(which in some embodiments is part of an array). In certain embodiments,the capture molecules have a pKa near neutral pH and are water solublein their protonated form and insoluble in their deprotonated form.Reactants can be attached to the capture molecules using any methodsknown in the art. A voltage can then be applied through an anode (502)in the solution to selectively deposit the capture molecules onto thebases of the nanoscale wells (503), which serves to also immobilize theattached reactants to the base of the nanoscale well. In otherembodiments, the capture molecules are first selectively deposited, andthen the reactants are attached to the capture molecules at the base ofthe nanoscale well. In further exemplary embodiments, the capturemolecules include without limitation chitosan and the reactants includecomplexes containing polymerase enzymes associated with template nucleicacids that are optionally hybridized to primers. In further embodiments,the method includes a step of exposing the nanoscale well to an aqueoussolution with pH less than 4 in order to remove the capture moleculesand attached reactants to prepare the nanoscale wells for delivery of anew set of capture molecules. In an embodiment related to that shown inFIG. 5 , a transparent conducting layer (e.g., an indium tin oxidelayer) forms the base of the nanoscale well and serves as the cathode.

As will be appreciated, the above-described electrodeposition method mayalso be performed through application of voltage by a cathode in thesolution layer above the nanoscale well. In such an embodiment, theconducting layer allows exposure of anodes at or near the base of eachnanoscale well, and the capture molecules are water soluble in theiruncharged form and insoluble in their charged form. As with the methoddescribed above, the attaching of reactants to the capture molecules canbe accomplished before application of the voltage for selectivedeposition or after application of the voltage.

For any of the electrodeposition methods described herein, the reactionsite may in some embodiments include a nanopore. An exemplary embodimentwould be if the device in FIG. 5 were to be drilled completely throughsuch that rather than having a base in the transparent insulator a poreis formed. The use of voltage for selective deposition above wouldequally apply to such nanopores, and the deposition would be within thenanopore.

In one exemplary embodiment, observation of biochemical reactions inzero-mode waveguides using electrodeposition methods involves theimmobilization of reactants at the base of the ZMW. The polysaccharidechitosan (deacetylated chitin) contains primary amino groups with pKa'sof about 6. The protonated form is water soluble, while the deprotonatedpolymer is insoluble. This feature enables selective deposition frommildly acidic solutions at the basic region generated around the cathodeunder applied voltage (Wu et al., 2002, Langmuir 18:8620-8625). Thisfeature has enabled the controlled assembly of chitosan hydrogels in avariety of micro fluidic devices (Kim et al., 2015, Polymers, 7:1-46).In addition to the polysaccharide, modified chitosans such asprotein-chitosan conjugates (Chen et al., 2003, Langmuir, 19:9382-9386)and biotin-chitosan conjugates (Shi et al., 2008, MacromolecularBioscience, 8:451-457) have also been directed to cathode surfacesthrough electrodeposition. The incorporation of a conducting layer in asurface (see FIG. 5 ) would allow exposure of cathodes to solution atthe base of each ZMW. Applying voltage through an anode in solutionpromotes the selective deposition of chitosan or chitosan derivatives atthe base of the ZMW, targeting molecules of interest to this location.If a transparent conductor such as indium tin oxide were layered belowan opaque insulating material, the upper layer of the chitosan hydrogelcould be in the observation volume of the waveguides. While stable inneutral solutions, these chitosan membranes can be resolubilized inmildly acidic solutions (pH<5). If the ZMW devices were fabricated to betolerant of exposure to aqueous solutions in the pH range of 4-8, theimmobilization surface could be removed and regenerated repeatedly.Chitosan has abundant reactive amines that have been coupled to avariety of biomolecules, and thus molecules of interest, includingnucleic acid templates and complexes containing polymerases and templatenucleic acids, can be readily attached via those reactive amines anddelivered to the base of the ZMWs with the above described process.

VI. Electrophoretic/Pressure

In some examples, the methods described herein utilize a mechanism inwhich template nucleic acids or other molecules of interest aredelivered to a reaction site, such as a nanoscale well, through theapplication of pressure or voltage. In one example, the reaction sitesare overlaid by an array of chambers such that the chambers line updirectly with the reaction sites. Voltage or pressure is used to drivemolecules into the chambers. Then, because the reaction sites willtypically have larger openings than the upper openings of the chambers,the molecules within the chambers are more likely to diffuse into thereaction site rather than out of the chambers.

The upper openings of the array of chambers optionally have diameters ofabout 20-100, 20-80, 25-75, 30-70, 35-65, 40-60, 20-50, 30-75 and 30-55nm. In yet further embodiments, the upper openings of the chambers havediameters of about 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85,90 nm.

As shown in FIG. 18A, chambers 1801 are conveniently fabricated as holesthrough layer or sheet 1803, e.g., that is aligned on top of substrate1805 in which nanoscale wells 1807 (e.g., ZMWs) are formed. Each chambercan be, e.g., cylindrical. More typically, however, the top opening ofthe chamber is smaller than the bottom opening, as shown in FIG. 18A.The opening of the nanoscale well is optionally smaller, larger, or thesame as the bottom opening of the chamber, but is typically larger thanthe top opening of the chamber. In one exemplary embodiment, the topopening of the chamber is 25-75 nm in diameter while the bottom openingof the chamber is 200-500 nm. In an exemplary embodiment, the depth ofthe chamber is 100-500 nm.

In another example, a fluid-filled chamber is located above the reactionsites, and a loading screen is provided to the top of the fluid-filledchamber, wherein the loading screen comprises randomly or nonrandomlyplaced holes. A solution containing template nucleic acids or othermolecules of interest is applied to the loading screen and then pressureor voltage is applied to the solution to drive the template nucleicacids into the fluid-filled chamber through the holes of the loadingscreen. The template nucleic acids then passively diffuse from thefluid-filled chamber into the nanoscale wells. The holes in the loadingscreen over the fluid filled chamber optionally have diameters of about20-100, 20-80, 25-75, 30-70, 35-65, 40-60, 20-50, 30-75 and 30-55 nm. Inyet further embodiments, the holes in the loading screen have diametersof about 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90 nm.

As shown in FIG. 18B, loading screen 1841 is conveniently fabricated asholes 1845 through a film or thin sheet. Screen 1841 overliesfluid-filled chamber 1843. Holes 1845 are optionally randomly placed asshown in FIG. 18B. In other embodiments, the holes are nonrandomlypositioned, e.g., to align with the openings of nanoscale wells 1847 insubstrate 1849. The holes are typically smaller in diameter than theopenings of the nanoscale wells. In one exemplary embodiment, the holesin the screen are 50 nm in diameter and the fluid-filled chamber has adepth of 150-500 nm.

For any of the embodiments involving loading through use ofelectrophoresis or pressure, the reaction sites may comprise an array ofnanoscale wells. The nanoscale wells will typically have openings largerthan the upper openings of the array of chambers or the holes in theloading screens. The applied electric field or pressure is optionallypulsed. Without limitation to any particular mechanism, such pulsing canload a small amount of nucleic acid into the chamber at a time toprevent entanglement.

For any of the methods described above, the molecules to be delivered tothe reaction sites may include template nucleic acids, e.g., in complexwith polymerase enzymes and/or primers. In still further embodiments,the template nucleic acids are about 3-30, 5-20, 7-10, 7-15 kb inlength.

Further exemplary embodiments of approaches to electrophoretic loadingare provided in FIGS. 6-11 . These embodiments include several methodsto achieve direct loading through an applied voltage between (1) aconducting functionalized substrate; (2) the metal cladding of anear-field aperture array (ZMW); (3) a polarized electrode; (4) anembedded layer in the substrate and counter electrode in solution.Although the following descriptions are provided in terms of ZMWs, itwill be appreciated that any reaction sites can be used in thesemethods.

FIG. 6A shows a schematic of approach (1) (A conducting functionalizedsubstrate). The substrate, which is typically fused silica, could bemade of any optically transparent material (e.g. ITO). A barrier metaloxide layer serves to insulate the substrate from the metal cladding.The conducting substrate can be connected to a terminal of a suitablevoltage source (e.g. battery or potentiostat). A counter electrode (e.g.platinum wire) connects to the voltage supply to complete the circuit.In this manner, charged molecules (e.g. DNA) can be directed to (orfrom) the ZMW bottom due to the electric field-induced force (FIG. 6B),thereby increasing the local density proximal to the ZMWs andfacilitating loading into ZMWs (FIG. 6C). Optionally, the ZMW bottom maybe functionalized (e.g. biotinylated) for specific attachment of targetmolecules.

FIG. 7 shows a schematic of approach 2 (Electrode attachment to themetal cladding of a ZMW array). In this method, a voltage is appliedbetween the ZMW cladding metal and a counter electrode in solution.

FIG. 8 shows a schematic of approach 3 (A polarized electrode). In thismethod, a voltage is applied between a working electrode (e.g. platinumwire or sheet) and a counter electrode (e.g. platinum wire or sheet) insolution with a target ZMW array located in between.

FIG. 9 shows a schematic of approach 4 (an embedded layer within thesubstrate). In this method, a voltage is applied between a workingelectrode (e.g. platinum wire or sheet) and a counter electrodetransparent sheet under the substrate. Optionally, this sheet can beintegrated into an optode. Optionally, this sheet may form part of thewaveguide.

A potential applied across the electrodes enables controlled mobility ofcharged molecules in solution. This method can also be applied toindividual ZMWs through a counter electrode in solution and a workingelectrode underneath each ZMW (e.g. a conducting pad or ring) (FIG. 10). Optionally, these ZMW specific pads can be integrated into an optode.Optionally, these pads can be individually addressable or addressed asinterlaced arrays, possibly using existing ZMW-specific electricalconnections to the proximal detector or pulse-to-base processing unit.

Physical properties of the electrode/ZMW/chemistry composite can also bemonitored during active loading, e.g., capacitance, at various scalesfrom individual ZMWs to entire arrays of ZMWs. Physical properties thatchange when a complex loads into a given ZMW can also be monitored,e.g., capacitance (FIG. 11 ), which gives a direct readout of thecurrent loading status. For individual ZMWs, this can be used to achieveSuper Poisson loading, by facilitating loading per ZMW until loaded,then reversing the voltage to reject further loading (but not sostrongly that the loaded template gets ripped out of the ZMW).Optionally, the bias voltage that forces complex to the ZMWs could bemodulated, or the sign even reversed for short periods of time. For suchan AC signal, the relaxation time constant (1/RC) could be monitored,and a change in that signal corresponding to a loaded complex could bethe trigger to stop further loading into that ZMW. For ZMW arrays, thedesired loading can be targeted in real time, which could compensate forother factors that impact loading speed (e.g., template size variation,chip quality, ZMW size variation, etc.).

Any of the methods for electrophoretic loading may be combined with anyother loading methods described herein and known in the art, includingother electrophoretic loading methods such as those described forexample in PCT Publication No. WO 2013/096819.

In some embodiments, loading through electrophoresis or pressureincludes the use of entropic barriers to facilitate loading in reactionsites such as nanoscale wells. In general, such loading methods are usedwith a device configured to have at least one fluidic channel overlayinga nanoscale well (generally over an array of nanoscale wells), where thefluidic channel includes alternating thick and thin regions, e.g.,regions of differing degrees of confinement (with a lesser confinementrelating to “thick” regions and a greater degree of confinement relatingto “thin” regions). Voltage or pressure is used to drive nucleic acidsthrough the fluidic channel over the nanoscale well(s). The thin regionsof the channel serve as entropic barriers, such that upon application ofvoltage (electric potential) or pressure (including hydrodynamicpressure), a local increase in nucleic acid concentration occurs throughan entropic trapping effect. If the entropic barriers are positionedappropriately, this concentration increase can be situated above thereaction sites, thus improving the ability to load the reaction siteswith molecules of interest. Such methods can be particularly useful forloading nanoscale wells, such as ZMW's, which often pose loadingbarriers due to their own entropic barriers to entry that is a result oftheir relative scale to the surroundings and the molecules being loaded.An additional benefit of using entropic barriers is that the entropictrapping effect can preferentially concentrate longer molecules (e.g.,molecules whose radius of gyration is significantly greater than thedepth of the thin regions) and thus act to compensate forlength-dependent loading effects that tend to preferentially load smallfragments. In certain embodiments, the longer molecules that aresuccessfully loaded comprise nucleic acids on the order of kilobases ormegabases in length.

By judicious use of variations in the degrees of confinement along thedirection of flow, the directed loading of an individual molecule to anindividual sequencing location can also be developed. In general, thethin regions are sufficiently small to act as constrictions to the flowof small objects, such as DNA molecules, polymerase enzyme complexes,proteins, cells, viruses, or other similarly-sized particles, while thethick regions allow molecules to relax for more efficient collection atthe thin region. To this end, the thick region depth may be madecomparable to, or substantially larger than, the size of a molecule (forexample, the radius of gyration R_(o) for polymer molecules) to be movedthrough the manifold. Also the thin region depth may be madesubstantially smaller than the size of the molecule or other object tobe moved through the device (e.g., substantially less than R_(o)).Although this configuration of devices used in the methods describedherein can be used to load a variety of objects, much of the descriptionherein will be in terms of molecules, and particularly nucleic acidmolecules for convenience. Without being bound by theory, the entropicbarriers described herein help develop local concentrations of moleculesbecause the equilibrium spherical shape of a molecule such as DNA orprotein has a radius of gyration R_(o), which is the shape the moleculeassumes when it is relaxed in an open region, such as in the thickregions of the channel. If the molecule is forced to enter aconstriction that is much less than R_(o), the molecule has to bedeformed from its equilibrium shape. Since such a deformation isentropically unfavorable, an increased driving force is required toforce the molecule to enter the constriction. This effect is referred toas the entropic trapping of a long polymer, such as a nucleic acid. Thuscontrolling the driving force allows control over the movement of themolecules along the channel and where local increases of concentrationoccur due to regions of greater confinement (constrictions) that serveas entropic barriers.

One exemplary embodiment of a configuration that utilizes entropicbarriers is illustrated in FIG. 19 , which provides a side view of thenanoscale well and the overlaying channel. In such a configuration, theflow of nucleic acids (denoted by the arrow pointing from left to rightin FIG. 19 ) is tangential to the surface of a substrate, for examplesuch as one employed in the Pacific Biosciences Sequel System®. In thisarrangement, a nanofluidic manifold (designated “top manifold cover” inFIG. 19 ) is positioned over the substrate to form a channel positionedtangential to the surface of the substrate. The nanofluidic manifold hasvariations that produce changes in the height of the channel, creatingzones of lesser and greater confinement—e.g., “thick” and “thin”regions.

In embodiments utilizing voltage to move the nucleic acid moleculesalong the length of the channel, electrodes can be positioned at eitherend of the manifold to provide an electrophoretic force to drivemolecules through the device. An aspect of the entropic trap array isthat a drive voltage below a certain threshold will allow passagethrough the larger region of the channel (the “thick” region), butmolecules above a certain size will not pass through the smaller regionof the channel (the “thin” region). Above the voltage threshold,molecules will pass through both thick and thin regions withoutstopping. The threshold voltages can be easily identified and utilizedbased on the size of the molecules that are desired for loading into thereaction sites.

In a first phase of operation, a high driving force is applied to loadmolecules throughout the manifold. Then, in a second phase, the drivingforce is reduced so that the molecules collect at the next region ofgreater confinement (thin region). This will cause an increase inconcentration which is proportional to the volume of the portion of themanifold between the two neighboring regions of greater confinement. Bypositioning the thin regions next to the nanoscale wells, the secondphase of the driving force thus favors loading of the nanoscale wellsthrough that local increase in concentration (see FIG. 19 ).

As will be appreciated, the configuration of the entropic barriers caninclude any combination of thick and thin regions of greater and lesserconfinement that are useful for loading one or more nanoscale wells withmolecules of interest (such as nucleic acids). FIGS. 20-22 illustratefurther exemplary embodiments of this aspect of the invention forexemplary arrays of nanoscale wells. As will be appreciated, althoughthe discussion herein is primarily in terms of nanoscale wells for easeof discussion, any other configuration of reaction sites is encompassedby the methods and configurations described herein.

FIG. 20 shows a top-view of an “open channel” configuration in which anarray of nanoscale wells (2002) is overlaid by an open channel formed bya wall (2004) on each side of the array—this open channel contains thinregions of greater confinement that form entropic barriers (2003) justafter each row of nanoscale wells along the direction of flow (2001).These entropic barriers thus increase the concentration of nucleic acids(2005) over or in close proximity to the nanoscale wells (2002), thusincreasing the probability that the nucleic acids are able to diffuseinto the nanoscale wells. The exemplary configuration pictured in FIG.20 shows a driving force that comprises voltage (an electricalpotential) that serves to move the nucleic acids from the cathode end ofthe device toward the anode end. As will be appreciated, the directionof flow could be changed by reversing the electrical potential. Infurther embodiments, the same open channel configuration can be used inaccordance with FIG. 20 , but the driving force is provided byhydrodynamic pressure rather than electrical potential. In such anembodiment, the regions of greater confinement work as entropic barriersin the same way as when electrical potential is used as a driving force.In further embodiments, the open channel is large enough to cover theentire array of nanoscale wells. In certain embodiments, the openchannel may cover part of the array but leave certain nanoscale wellsfree of the overlaying channel. Note that FIG. 20 is not drawn to scale,and that any combination of widths and degrees of confinement can beused as long as the ratio between the regions of greater and lesserconfinement serve to set up entropic barriers that help to concentratethe nucleic acids at or near the regions of greater confinement, therebyincreasing the probability of loading of nearby nanoscale wells with thenucleic acids.

FIG. 21 shows a top-view of an “closed channel” configuration in whichan array of nanoscale wells (2102) is overlaid by a series of closedchannels formed by walls (2103) separating columns of nanoscale wellsfrom each other. Each of the channels contains regions of greaterconfinement that form entropic barriers (2104), such that as nucleicacids are driven along the array in a desired direction (2101), theentropic barriers increase the concentration of nucleic acids over or inclose proximity to the nanoscale wells, thus increasing the probabilitythat the nucleic acids are able to diffuse into the nanoscale wells. Aswith the configuration illustrated in FIG. 20 , the driving force in aclosed channel configuration such as that pictured in FIG. 21 can be anelectric potential (illustrated in the figure by driving from a cathodeend to an anode end) or by hydrodynamic pressure. In certainembodiments, the number of channels overlaying the array is equal to thenumber of columns of nanoscale wells that are present in the array, suchthat every nanoscale well is overlaid by a channel. Note that FIG. 21 isnot drawn to scale, and that any combination of widths and degrees ofconfinement can be used as long as the ratio between the regions ofgreater and lesser confinement serve to set up entropic barriers thathelp to concentrate the nucleic acids and thereby increase theprobability of loading of the nanoscale wells with the nucleic acids.

FIGS. 20-21 illustrate embodiments in which the entropic barriers areconfigured to be at right angles to the flow path of the nucleic acidmolecules (and the surface of the substrate housing the nanoscalewells). As will be appreciated, any configuration that develops anentropic barrier is encompassed by the disclosed invention. A furtherexemplary embodiment is illustrated in FIG. 22 . FIG. 22 is a top viewof a single nanoscale well (ZMW) in which the entropic barrier is formedas a chevron shape in which the sides of the entropic barrier angletoward the ZMW. An advantage of such a configuration is that in additionto increasing the local concentration near the nanoscale wells, theshape of the entropic barrier further enhances loading by disturbing thedriving force such that it favors the “point” of the chevron, which isover or near the entrance of the nanoscale well. Although FIG. 22illustrates an embodiment in which the molecule of interest being driventoward the ZMW is DNA, it will be appreciated that any charged moleculecan be used in any of the configurations described herein when anelectric potential is used as the driving force. When hydrodynamicpressure is used as the driving force, any molecule susceptible to sucha force can also be used in this or any other configuration describedherein. FIG. 22 illustrates an embodiment in which the open channelconfiguration is used, such as that illustrated in FIG. 20 —however,similar chevron-shaped entropic barriers may also be used with theclosed channel configuration such as that illustrated in FIG. 21 .

For any of the configurations described herein for utilizing entropicbarriers to assist in loading of nanoscale wells, the thin regions ofgreater confinement that function as entropic barriers can have anydepth the serves to delay or substantially prevent the progress ofmolecules of interest, particularly charged molecules such as nucleicacids e.g., in polymerase enzyme complexes. In certain embodiments, theregions of greater confinement have a depth of about 1 nm to about 1000nm. In further embodiments, the regions have a depth of about 10-900,20-800, 30-700, 40-600, 10-500, 50-500, 60-400, 70-300, 80-200, 50-200,90-100 nm. In still further embodiments, the regions have a depth ofabout 2-100, 2-50, 4-50, 30-50, 5-500, 5-10, 20-40, 80-120, 300-500,100-600 nm. In yet further embodiments, the regions have a depth ofabout 2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 500, 750,1000, 1250, 1500 nm. The thick regions of lesser confinement have adepth greater than that of the thin regions. In certain embodiments, thethick regions have a depth between about 0.5 μm and about 10 μm.

The material of the manifold and the substrate housing the nanoscalewells can comprise any suitable material that is conducive to use in themethods described above. Materials and techniques suitable forfabrication of the manifold are known in the art; see, e.g., U.S. Pat.No. 7,918,979. In certain embodiments, the top manifold is made out of atransparent material, and the molecules are labeled, for example with anintercalant dye. Such a configuration allows the observation of themolecules as they flow across the array of nanoscale wells in real-time.An advantage provided by this ability to observe the molecules in realtime is that the loading of the nanoscale wells can be tracked—if wellsare not loaded during the first pass through the array (which can bedetected by observing the pattern of molecules left on the array), thenthe direction of the driving force can be reversed to allow another passover the nanoscale wells with the molecules. This reversal and passthrough of the detectable molecules can be repeated until the desiredpercentage of nanoscale wells in the array is loaded. As will beappreciated, any type of label or method that allows observation andmonitoring of the movement of the nucleic acids in real time can be usedto perform this aspect of the invention.

In further embodiments, and in accordance with any of the embodimentsdescribed above, it will be appreciated that the reaction sites mayinclude any of the other types of molecules and configurations describedherein such that loading of the reaction sites is further enhanced bysuch combinations and/or in order to include items in the reaction sitesfor downstream use of the reaction sites and the loaded nucleic acids.For example, the reaction sites may include capture moieties and/orother tethering molecules, such as those described above, which caninteract with the nucleic acids or polymerase enzyme complexes andfurther encourage loading of the reaction sites with the nucleic acidsor complexes. The reaction sites may further include polymerase enzymesand other reagents for use in downstream sequencing reactions once thenucleic acids are loaded.

In still further embodiments, configurations for use in accordance withany of the above described methods for utilizing entropic barriersfurther include devices, systems and methods described in the art formolecular sieving and trapping, including for example U.S. Pat. Nos.7,918,979 and 6,635,163, which are herein incorporated by reference intheir entirety for all purposes and in particular for all teachings andfigures related to separation of molecules. In yet further embodiments,the entropic barrier methods described herein are not operated such thatthe barriers act as a “sieve” to separate certain molecules from others,but are instead used to concentrate molecules, particularly largermolecules, at certain regions along the path of flow of the drivingforce.

VII. Affinity Loading

In some aspects, the methods described herein utilize a processinvolving affinity loading. In general, a surface containing reactionsites, such as nanoscale wells, is coated with a positively chargedpeptide. A composition containing molecules of interest that havenegative charges (such as nucleic acid templates or polymerase enzymecomplexes) is applied to the coated surface such that at least a portionof the molecules attach to the positively charged peptides (seeschematic illustration in FIG. 12 ). This attachment increases theeffective local concentration of the molecules of interest near thereaction sites. The molecules are then released from the positivelycharged surface to allow the molecules to passively diffuse into thereaction sites. A higher percentage of the molecules will load into thereaction sites than is seen with passive diffusion alone, because of thestep of increasing the effective local concentration near the sitesthrough affinity attachment to the positively charged peptides.

In specific aspects, these affinity loading methods include the steps ofproviding a surface comprising an array of nanoscale wells; coating thatsurface with a positively charged peptide to form a coated surface;applying a composition comprising polymerase enzyme complexes to thecoated surface such that at least a portion of the polymerase enzymecomplexes attach to the positively charged peptides; and releasing thepolymerase enzyme complexes from the positively charged peptides orpolypeptides to allow the polymerase enzyme complexes to passivelydiffuse into the nanoscale wells.

The releasing step generally involves applying a composition to thesurface that can weaken or break the attachment between the molecules ofinterest and the positively charged peptides. For example, release canbe accomplished by applying a protease (e.g., trypsin) to the surface todigest the positively charged peptide and release the polymerase enzymecomplexes. As another example, the complexes can be released by elutionwith high salt (e.g., 500 mM potassium acetate).

In some embodiments, loading efficiency can be further improved byapplying size exclusion resin to the surface, e.g., after application ofthe complexes to the coated surface and prior to elution of thecomplexes. For example, Sephadex G100 size exclusion resin can beapplied to the surface (e.g., by application to a liquid layer overlyingthe surface). Without limitation to any particular mechanism, additionof the size exclusion resin can improve loading by effectivelyincreasing the concentration of the polymerase-template complexes in theexcluded volume and/or by acting as a barrier that slows diffusion ofthe complexes away from the surface after they have been eluted from thecoating.

In general, the positively charged peptides or polypeptides that areapplied to the surface can comprise anything that would provide a coatedsurface with an overall positive charge that is able to attract themolecules of interest for attachment near the reaction sites. Suchpeptides or polypeptides can include without limitation Tat,poly-lysine, poly-arginine, and histone. Peptides rich in arginine,lysine, and histidine may also be used. For peptides rich in histidine,loading would be conducted at pH below ˜6. Deprotonation at a higher pHwould then cause release from the surface when using such histidine-richpeptides. Non-peptide compositions, including cationic polymers (e.g.,cationic branched polyethylene glycols), can also be employed.

In specific embodiments, the molecules loaded in the above-describedaffinity loading methods include polymerase enzyme complexes comprisingpolymerase enzymes attached to template nucleic acid molecules. Infurther embodiments, the template nucleic acid molecules are hybridizedto a primer.

In further embodiments, the template nucleic acid molecules are at least3, 5, 7, 10, 15, 20, 25, 30, 35, 40, 45, 50 kb long. In furtherembodiments, the template nucleic acid molecules are about 3-20, 5-15,6-10, 2-25, 1-30 kb long.

These affinity loading methods generally result in loading of themolecules of interest, including polymerase enzyme complexes, at ratesthat are about 2-20, 4-15, 6-10, 10-150, 20-140, 30-130, 40-120, 50-110,60-100, 70-80 times faster than seen with diffusion loading alone. Infurther embodiments, the affinity loading methods result in loading ofat least 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200,250, 300, 350, 400, or 500 times faster than seen with diffusion loadingalone. Without limitation to any particular mechanism, these affinityloading methods can favor loading of larger (e.g., at least 5000 bp)templates over smaller templates (e.g., less than 2000 or 1000 bp).

In specific embodiments, the affinity loading method includes steps ofpre-coating a surface containing reaction sites (the surface will insome embodiments comprise a predominantly negatively charged materialsuch as TiN or Al) with positively charged peptides (e.g., Tat,poly-lysine, histones). This coating will serve to condense complexescontaining template nucleic acids and polymerases near and onto thesurface. Once localized near the surface (which may contain biotinbinding sites for capture of streptavidin-associated complexes), thecomplexes can be released (or affinity weakened) with a high saltelution step. This approach results in an increased local concentrationand dwell time and has been shown to greatly improve loading whencompared to diffusion loading.

In further embodiments and in accordance with any of the description foraffinity loading methods described above, the positive charges may bedesigned to localize specifically to the reaction sites (such as ZMWs,particularly the bases of ZMWs), for more effective recruitment of themolecules of interest. In an exemplary embodiment, the reaction sitesare selectively coated with streptavidins containing cysteines that havebeen labeled with a maleimide containing high molecular weightpolylysine. The polylysine can help attract the DNA in a templatenucleic acid such as a SMRTbell™. After the template nucleic acid (andany associated molecules such as polymerase enzymes) have beeneffectively loaded into the reaction sites, the polylysine can beremoved prior to downstream analyses such as sequencing reaction throughapplication of a protease such as trypsin. Similar methods can beaccomplished using other coating materials such as polyarginine or anyother composition that has affinity for both DNA and the reactionregion. In further examples, the molecule/complex of interest can becoupled to a peptide that has affinity for the surface of a reactionsite such as a ZMW, particularly the ZMW base (including anyfunctionalization at the reaction site and/or binding moieties at thereaction site). In further embodiments, affinity for the ZMW base can bethrough a specific interaction such as biotin on the template nucleicacid or polymerase binding to streptavidin on the surface of the ZMWbase (or vice versa) or through differential affinity for the ZMW base(which generally comprises a silica-based material) over the rest of thesurface (which generally comprises metal or metal oxide). In furtherembodiments, phage display can be used to select peptides with affinityfor various oxide surfaces. (See Seker et al., Molecules, 2011, 16:1426-1461). Such peptides can be fused to molecules having affinity fornucleic acids (or other molecules of interest). In still furtherembodiments, affinity for the molecule of interest, particularly for acomplex containing a nucleic acid template complexed with a polymerase,may be designed through the use of a nonspecific DNA binding proteinselectively deposited at the reaction site (e.g., through specific ordifferential binding as described above). In other embodiments, any ofthe charged peptides and polypeptides discussed herein, including Tat,polylysine and polyarginine, can supply affinity for thetemplate/polymerase complex or other molecule of interest. Fusionpeptides including streptavidin-Tat, or streptavidin bound tobiotinylated Tat, could also be used in accordance with any of themethods described herein as molecules for selective distribution ofmolecules of interest to a reaction site (e.g a biotinylated ZMW base).

In still further embodiments the affinity loading methods describedherein can be combined with any other Super Poisson loading methodsand/or density loading methods known in the art and described forexample in U.S. Pat. No. 8,906,831, U.S. Ser. No. 15/078,915, filed Mar.23, 2016 and U.S. Ser. No. 62/257,152, filed Nov. 18, 2015, herebyincorporated by reference in their entirety for all purposes and inparticular for all teachings related to methods and compositions forloading reaction sites, such as nanoscale wells, with molecules ofinterest, such as polymerase enzyme-template complexes.

VIII. Compositions

VIIIA. Template Molecules

Any of the methods and complexes described herein can include templatenucleic acid molecules (also referred to herein as “templatesequences”), often as part of the polymerase enzyme complexes describedherein. In general, the template nucleic acid is the molecule for whichthe complementary sequence is synthesized in the polymerase reaction. Insome cases, the template nucleic acid is linear; in some cases, thetemplate nucleic acid is circular. The template nucleic acid can be DNA,RNA, and/or a non-natural RNA or DNA analog. Any template nucleic acidthat is suitable for replication by a polymerase enzyme can be used inthe methods and systems described herein.

In some embodiments, the template nucleic acids used in methods andcompositions of the present invention comprise nucleic acids obtainedfrom a sample. The sample may comprise any number of things, including,but not limited to, bodily fluids (including, but not limited to, blood,urine, serum, lymph, saliva, anal and vaginal secretions, perspirationand semen) and cells of virtually any organism, with mammalian samplesbeing preferred and human samples being particularly preferred;environmental samples (including, but not limited to, air, agricultural,water and soil samples); biological warfare agent samples; researchsamples (i.e. in the case of nucleic acids, the sample may be theproducts of an amplification reaction, including both target and signalamplification, such as PCR amplification reactions; purified samples,such as purified genomic DNA, RNA preparations, raw samples (bacteria,virus, genomic DNA, etc.); as will be appreciated by those in the art,virtually any experimental manipulation may have been done on thesamples.

In further embodiments, nucleic acid molecules are obtained from asample and fragmented for use in methods of the invention as templatenucleic acids. The fragments may be single or double stranded and mayfurther be modified in accordance with any methods known in the art anddescribed herein. Template nucleic acids may be generated by fragmentingsource nucleic acids, such as genomic DNA, using any method known in theart. In one embodiment, shear forces during lysis and extraction ofgenomic DNA generate fragments in a desired range. Also encompassed bythe invention are methods of fragmentation utilizing restrictionendonucleases.

As will be appreciated, the template nucleic acids may be generated froma source nucleic acid, such as genomic DNA, by fragmentation to producefragments of a specific size. The target nucleic acids can be, forexample, from about 10 to about 100,000 nucleotides in length, fromabout 10 to about 50,000 nucleotides in length, or from about 10 toabout 20,000 nucleotides in length. In one embodiment, the fragments are50 to 600 nucleotides in length. In another embodiment, the fragmentsare 300 to 600 or 200 to 2000 nucleotides in length. In yet anotherembodiment, the fragments are 10-100, 50-100, 50-300, 100-200, 200-300,50-400, 100-400, 200-400, 400-500, 400-600, 500-600, 50-1000, 100-1000,200-1000, 300-1000, 400-1000, 500-1000, 600-1000, 700-1000, 700-900,700-800, 800-1000, 900-1000, 1500-2000, 1750-2000, and 50-2000nucleotides in length. In further embodiments, the fragments are atleast 5000, 10000, 15000, 20000, 25000, 30000, 40000, 50000, 60000,70000, 80000, 90000, 100,000, 120,000, 130,000, 140,000, or 150,000nucleotides in length. In yet further embodiments, the nucleic acidtemplates are 10-100, 50-100, 50-300, 100-200, 200-300, 50-400, 100-400,200-400, 400-500, 400-600, 500-600, 50-1000, 100-1000, 200-1000,300-1000, 400-1000, 500-1000, 600-1000, 700-1000, 700-900, 700-800,800-1000, 900-1000, 1500-2000, 1750-2000, 50-2000, 100-25000, 200-24000,300-23000, 400-22000, 500-21000, 600-20000, 700-19000, 800-18000,900-17000, 1000-16000, 1100-15000, 1200-14000, 1300-13000, 1400-12000,1500-11000, 1600-10000, 1700-9000, 1800-8000, 1900-7000, 2000-6000,2100-5000, 2200-4000, 2300-3000, 5000-20000, 10000-30000, 12000-28000,14000-26000, 16000-24000, 18000-22000, 19000-20000, 20000-40000, or40000-60000 nucleotides in length. In yet further embodiments, thenucleic acid templates are at least 5000, 10000, 15000, 20000, 25000,30000, 40000, 50000, 60000, 70000, 80000, 90000, 100,000, 120,000,130,000, 140,000, or 150,000 nucleotides in length. In furtherembodiments, the nucleic acid templates are part of polymerase-templatecomplexes. In yet further embodiments, the nucleic acid templates arethemselves further hybridized to primers.

In some cases, the template sequence may be a linear single or doublestranded nucleic acid sequence. In still other embodiments, the templatemay be provided as a circular or functionally circular construct thatallows redundant processing of the same nucleic acid sequence by thesynthesis complex. Use of such circular constructs has been describedin, e.g., U.S. Pat. No. 7,315,019 and U.S. patent application Ser. No.12/220,674, filed Jul. 25, 2008, and alternate functional circularconstructs are also described in US Pat. App. Pub. No. 20090298075, thefull disclosures of each of which are incorporated herein by referencein their entirety for all purposes and in particular for all teachingsrelated to template nucleic acid constructs. Briefly, such alternateconstructs include template sequences that possess a central doublestranded portion that is linked at each end by an appropriate linkingoligonucleotide, such as a hairpin loop segment. Such structures notonly provide the ability to repeatedly replicate a single molecule (andthus sequence that molecule), but also provide for additional redundancyby replicating both the sense and antisense portions of the doublestranded portion. In the context of sequencing applications, suchredundant sequencing provides great advantages in terms of sequenceaccuracy.

In further aspects, the template nucleic acid used in the compositionsof the present invention includes: a double stranded nucleic acidsegment having a first and second end; a first hairpin oligonucleotideconnecting each strand of the single template nucleic acid at the firstend; a second hairpin oligonucleotide connecting each strand of thesingle template nucleic acid at the second end. In some embodiments, thefirst hairpin and second hairpin oligonucleotide are identical. In otherembodiments, the first hairpin and second hairpin oligonucleotides arenot identical—in other words, the template nucleic acid, despite beingan alternate circular construct, is nevertheless asymmetrical. Infurther embodiments, the first hairpin oligonucleotide includes a primerbinding site whereas the second hairpin oligonucleotide includes acapture adapter (or vice versa). The capture adapter is generally of asequence that can be used to enrich a population for the hairpins ofchoice—for example, in some embodiments, the capture adapter comprises apolyA sequence, thereby allowing capture using beads or columnchromatography utilizing polyT sequences. In other embodiments, thecapture adapter comprises at least one methoxy residue. In furtherembodiments, the capture adapter is complementary to an oligonucleotideattached to a bead, which can in further embodiments be a magnetic beadthat can be used to enrich a population for template nucleic acidscontaining the capture adapter. In some embodiments in which thepopulation of templates includes templates with different adapters or inwhich each template comprises a different adapter at each end, differentbeads can be used which contain oligonucleotides complementary to thedifferent adapters. Thus, for templates with two different adapters, twodifferent beads can be used. For populations containing a plurality ofdifferent adapters, a concomitant number of different types of beads canbe used that are directed to those adapters. In other embodiments, thesame bead can contain different oligonucleotides complementary to thedifferent adapters in the population of templates, such that the samebead can capture different adapters (and their associated templates).

In still further embodiments, the first or second hairpin comprises aself-primed adapter sequence in which the primer is part of the adapter.In such embodiments, an additional oligonucleotide primer is not neededto allow a polymerase molecule to begin replicating the template.

In yet further embodiments, the nucleic acid template contains only asingle hairpin at one end or the other.

VIII. B. Nucleotides and Nucleotide Analogs

Nucleotides of use in the present invention include, e.g., naturallyoccurring nucleotides such as dATP, dCTP, dGTP, and dTTP. Variousnucleotide analogs are also of use in the present invention. Uponincorporation into a growing oligonucleotide chain, the analog can leavea residue that is the same as or different than a natural nucleotide inthe growing oligonucleotide (the polymerase can incorporate anynon-standard moiety of the analog, or can cleave it off duringincorporation into the oligonucleotide). A “nucleotide analog” herein isa compound, that, in a particular application, functions in a mannersimilar or analogous to a naturally occurring nucleoside triphosphate (a“nucleotide”), and does not otherwise denote any particular structure. Anucleotide analog is an analog other than a standard naturally occurringnucleotide, i.e., other than A, G, C, T, or U, though upon incorporationinto the oligonucleotide, the resulting residue in the oligonucleotidecan be the same as (or different from) an A, G, C, T, or U residue.

In one useful aspect of the invention, nucleotide analogs can bemodified to achieve any of the improved properties desired. For example,various linkers or other substituents can be incorporated into analogsthat have the effect of reducing branching fraction, improvingprocessivity, or altering rates. Modifications to the analogs caninclude extending the phosphate chains, e.g., to include a tetra-,penta-, hexa- or heptaphosphate group, and/or adding chemical linkers toextend the distance between the nucleotide base and the dye molecule,e.g., a fluorescent dye molecule. Substitution of one or morenon-bridging oxygen in the polyphosphate, for example with S or BH₃, canchange the polymerase reaction kinetics, e.g., to achieve a systemhaving two slow steps as described hereinbelow. Optionally, one or more,two or more, three or more, or four or more non-bridging oxygen atoms inthe polyphosphate group of the analog has an S substituted for an O.While not being bound by theory, it is believed that the properties ofthe nucleotide, such as the metal chelation properties,electronegativity, or steric properties, can be altered by substitutionof the non-bridging oxygen(s).

Many nucleotide analogs are available and can be incorporated bypolymerases. These include analog structures with core similarity tonaturally occurring nucleotides, such as those that comprise one or moresubstituent on a phosphate, sugar, or base moiety of the nucleoside ornucleotide relative to a naturally occurring nucleoside or nucleotide.In one embodiment, the nucleotide analog includes three phosphatecontaining groups; for example, the analog can be a labeled nucleosidetriphosphate analog and/or an α-thiophosphate nucleotide analog havingthree phosphate groups. In one embodiment, a nucleotide analog caninclude one or more extra phosphate containing groups, relative to anucleoside triphosphate. For example, a variety of nucleotide analogsthat comprise, e.g., from 4-6 or more phosphates are described in detailin US patent application publication 2007-0072196, incorporated hereinby reference in its entirety for all purposes. Other exemplary usefulanalogs, including tetraphosphate and pentaphosphate analogs, aredescribed in U.S. Pat. No. 7,041,812, incorporated herein by referencein its entirety for all purposes.

For example, the analog can include a labeled compound of the formula:

wherein B is a nucleobase (and optionally includes a label); S isselected from a sugar moiety, an acyclic moiety or a carbocyclic moiety(and optionally includes a label); L is an optional detectable label; R₁is selected from O and S; R₂, R₃ and R₄ are independently selected fromO, NH, S, methylene, substituted methylene, C(O), C(CH₂), CNH₂, CH₂CH₂,and C(OH)CH₂R where R is 4-pyridine or 1-imidazole, provided that R₄ mayadditionally be selected from

R₅, R₆, R₇, R₈, R₁₁ and R₁₃ are, when present, each independentlyselected from O, BH₃, and S; and R₉, R₁₀ and R₁₂ are independentlyselected from O, NH, S, methylene, substituted methylene, CNH₂, CH₂CH₂,and C(OH)CH₂R where R is 4-pyridine or 1-imidazole. In some cases,phosphonate analogs may be employed as the analogs, e.g., where one ofR₂, R₃, R₄, R₉, R₁₀ or R₁₂ are not O, e.g., they are methyl etc. See,e.g., US patent application publication 2007-0072196, previouslyincorporated herein by reference in its entirety for all purposes.

The base moiety incorporated into the analog is generally selected fromany of the natural or non-natural nucleobases or nucleobase analogs,including, e.g., purine or pyrimidine bases that are routinely found innucleic acids and available nucleic acid analogs, including adenine,thymine, guanine, cytosine, uracil, and in some cases, inosine. Asnoted, the base optionally includes a label moiety. For convenience,nucleotides and nucleotide analogs are generally referred to based upontheir relative analogy to naturally occurring nucleotides. As such, ananalog that operates, functionally, like adenosine triphosphate, may begenerally referred to herein by the shorthand letter A. Likewise, thestandard abbreviations of T, G, C, U and I, may be used in referring toanalogs of naturally occurring nucleosides and nucleotides typicallyabbreviated in the same fashion. In some cases, a base may function in amore universal fashion, e.g., functioning like any of the purine basesin being able to hybridize with any pyrimidine base, or vice versa. Thebase moieties used in the present invention may include the conventionalbases described herein or they may include such bases substituted at oneor more side groups, or other fluorescent bases or base analogs, such as1,N6 ethenoadenosine or pyrrolo C, in which an additional ring structurerenders the B group neither a purine nor a pyrimidine. For example, incertain cases, it may be desirable to substitute one or more side groupsof the base moiety with a labeling group or a component of a labelinggroup, such as one of a donor or acceptor fluorophore, or other labelinggroup. Examples of labeled nucleobases and processes for labeling suchgroups are described in, e.g., U.S. Pat. Nos. 5,328,824 and 5,476,928,each of which is incorporated herein by reference in its entirety forall purposes.

In the analogs, the S group is optionally a sugar moiety that provides asuitable backbone for a synthesizing nucleic acid strand. For example,the sugar moiety is optionally selected from a D-ribosyl, 2′ or 3′D-deoxyribosyl, 2′,3′-D-dideoxyribosyl, 2′,3′-D-didehydrodideoxyribosyl,2′ or 3′ alkoxyribosyl, 2′ or 3′ aminoribosyl, 2′ or 3′ mercaptoribosyl,2′ or 3′ alkothioribosyl, acyclic, carbocyclic or other modified sugarmoieties. A variety of carbocyclic or acyclic moieties can beincorporated as the “S” group in place of a sugar moiety, including,e.g., those described in U.S. Patent Application Publication No.2003/0124576, which is incorporated herein by reference in its entiretyfor all purposes.

For most cases, the phosphorus containing chain in the analogs, e.g., atriphosphate in conventional NTPs, is preferably coupled to the 5′hydroxyl group, as in natural nucleoside triphosphates. However, in somecases, the phosphorus containing chain is linked to the S group by the3′ hydroxyl group.

L generally refers to a detectable labeling group that is coupled to theterminal phosphorus atom via the R₄ (or R₁₀ or R₁₂ etc.) group. Thelabeling groups employed in the analogs of the invention may compriseany of a variety of detectable labels. Detectable labels generallydenote a chemical moiety that provides a basis for detection of theanalog compound separate and apart from the same compound lacking such alabeling group. Examples of labels include, e.g., optical labels, e.g.,labels that impart a detectable optical property to the analog,electrochemical labels, e.g., labels that impart a detectable electricalor electrochemical property to the analog, and physical labels, e.g.,labels that impart a different physical or spatial property to theanalog, e.g., a mass tag or molecular volume tag. In some cases,individual labels or combinations may be used that impart more than oneof the aforementioned properties to the analogs of the invention.

Optionally, the labeling groups incorporated into the analogs compriseoptically detectable moieties, such as luminescent, chemiluminescent,fluorescent, fluorogenic, chromophoric and/or chromogenic moieties, withfluorescent and/or fluorogenic labels being preferred. A variety ofdifferent label moieties are readily employed in nucleotide analogs.Such groups include, e.g., fluorescein labels, rhodamine labels, cyaninelabels (i.e., Cy3, Cy5, and the like, generally available from theAmersham Biosciences division of GE Healthcare), and the Alexa family offluorescent dyes and other fluorescent and fluorogenic dyes availablefrom Molecular Probes/Invitrogen, Inc. and described in ‘The Handbook— AGuide to Fluorescent Probes and Labeling Technologies, Eleventh Edition’(2010) (available from Invitrogen, Inc./Molecular Probes). A variety ofother fluorescent and fluorogenic labels for use with nucleosidepolyphosphates, and which would be applicable to the nucleotide analogsincorporated by the polymerases of the present invention, are describedin, e.g., U.S. Patent Application Publication No. 2003/0124576,previously incorporated herein by reference in its entirety for allpurposes.

Thus, in one illustrative example, the analog can be a phosphate analog(e.g., an analog that has more than the typical number of phosphatesfound in nucleoside triphosphates) that includes, e.g., an Alexa dyelabel. For example, an Alexa488 dye can be labeled on a delta phosphateof a tetraphosphate analog (denoted, e.g., A488dC4P or A488dA4P, for theAlexa488 labeled tetraphosphate analogs of C and A, respectively), or anAlexa568 or Alexa633 dye can be used (e.g., A568dC4P and A633dC4P,respectively, for labeled tetraphosphate analogs of C or A568dT6P for alabeled hexaphosphate analog of T), or an Alexa546 dye can be used(e.g., A546dG4P), or an Alexa594 dye can be used (e.g., A594dT4P). Asadditional examples, an Alexa555 dye (e.g., A555dC6P or A555dA6P), anAlexa 647 dye (e.g., A647dG6P), an Alexa 568 dye (e.g., A568dT6P),and/or an Alexa660 dye (e.g., A660dA6P or A660dC6P) can be used in,e.g., single molecule sequencing. Similarly, to facilitate colorseparation, a pair of fluorophores exhibiting FRET (fluorescenceresonance energy transfer) can be labeled on a delta phosphate of atetraphosphate analog (denoted, e.g., FAM-amb-A532dG4P orFAM-amb-A594dT4P).

As noted above, an analog can include a linker that extends the distancebetween the nucleotide base and the label moiety, e.g., a fluorescentdye moiety. Exemplary linkers and analogs are described in U.S. Pat. No.7,968,702. Similarly, a protein or other moiety can be employed toprovide spacing and/or shielding between the base and the label, e.g.,as described in U.S. patent application Ser. No. 13/767,619 “PolymeraseEnzyme Substrates with Protein Shield” filed Feb. 14, 2013, and U.S.patent application Ser. No. 14/452,497 “Protected Fluorescent ReagentCompounds” filed Aug. 5, 2013. Suitable polymerase substrates optionallyinclude two or more nucleoside polyphosphates and/or two or more labelmoieties, e.g., as described in U.S. patent application Ser. No.13/767,619 “Polymerase Enzyme Substrates with Protein Shield,” U.S.patent application Ser. No. 14/452,497 “Protected Fluorescent ReagentCompounds,” and US patent application publication 2009-0208957 AlternateLabeling Strategies for Single Molecule Sequencing.

Additional details regarding labels, analogs, and methods of making suchanalogs can be found in US patent application publication 2007-0072196,WO 2007/041342 Labeled Nucleotide Analogs and Uses Therefor, WO2009/114182 Labeled Reactants and Their Uses, US patent applicationpublication 2009-0208957 Alternate Labelling Strategies for SingleMolecule Sequencing, U.S. patent application Ser. No. 13/218,412Functionalized Cyanine Dyes, U.S. patent application Ser. No. 13/218,395Functionalized Cyanine Dyes, U.S. patent application Ser. No. 13/218,428Cyanine Dyes, U.S. patent application Ser. No. 13/218,382 Scaffold-BasedPolymerase Enzyme Substrates, US patent application publication2010-0167299 Phospholink Nucleotides for Sequencing Applications, USpatent application publication 2010-0152424 Modular NucleotideCompositions and Uses Therefor, U.S. patent application Ser. No.13/767,619 “Polymerase Enzyme Substrates with Protein Shield,” and U.S.patent application Ser. No. 14/452,497 “Protected Fluorescent ReagentCompounds,” each of which is incorporated herein by reference in itsentirety for all purposes.

VIII. C. Polymerases

The methods and compositions of the present disclosure utilizepolymerase enzymes (also referred to herein as “polymerases”). Anysuitable polymerase enzyme can be used in the systems and methodsdisclosed herein. Suitable polymerases include DNA dependent DNApolymerases, DNA dependent RNA polymerases, RNA dependent DNApolymerases (reverse transcriptases), and RNA dependent RNA polymerases.In certain embodiments, the polymerases used in the methods andcompositions of the present invention are strand-displacing polymerases.

As disclosed in further detail herein, polymerases of use in thepresently disclosed methods may include modifications that improvecertain characteristics of the enzyme, including processivity,resistance to photodamage, and conduciveness to immobilization. Incertain aspects, polymerases used in the methods and systems disclosedherein include a linker through which the polymerases (and any othermolecules they are complexed with, such as template nucleic acids andoptionally replication initiating moieties) can be immobilized onto asurface. In certain aspects, these linkers are resistant to cleavage bya protease. Such linkers can be designed in conjunction with choicesmade for protease treatment methods. For example, for the loadingmethods described herein that utilize the protease trypsin, polymerasesof use in such methods can be designed to include linkers that areresistant to digestion by trypsin, e.g., peptide linkers that contain nolysine or arginine side chains, which are recognition sites for trypsinactivity.

DNA polymerases are sometimes classified into six main groups based uponvarious phylogenetic relationships, e.g., with E. coli Pol I (class A),E. coli Pol II (class B), E. coli Pol III (class C), Euryarchaeotic PolII (class D), human Pol beta (class X), and E. coli UmuC/DinB andeukaryotic RAD30/xeroderma pigmentosum variant (class Y). For a reviewof recent nomenclature, see, e.g., Burgers et al. (2001) “Eukaryotic DNApolymerases: proposal for a revised nomenclature” J Biol Chem.276(47):43487-90. For a review of polymerases, see, e.g., Hübscher etal. (2002) “Eukaryotic DNA Polymerases” Annual Review of BiochemistryVol. 71: 133-163; Alba (2001) “Protein Family Review: Replicative DNAPolymerases” Genome Biology 2(1):reviews 3002.1-3002.4; and Steitz(1999) “DNA polymerases: structural diversity and common mechanisms” JBiol Chem 274:17395-17398. The basic mechanisms of action for manypolymerases have been determined. The sequences of literally hundreds ofpolymerases are publicly available, and the crystal structures for manyof these have been determined, or can be inferred based upon similarityto solved crystal structures of homologous polymerases. For example, thecrystal structure of ϕ29, a preferred type of parental enzyme to bemodified according to the invention, is available.

In addition to wild-type polymerases, chimeric polymerases made from amosaic of different sources can be used. For example, ϕ29 polymerasesmade by taking sequences from more than one parental polymerase intoaccount can be used as a starting point for mutation to produce thepolymerases of the invention. Chimeras can be produced, e.g., usingconsideration of similarity regions between the polymerases to defineconsensus sequences that are used in the chimera, or using geneshuffling technologies in which multiple ϕ29-related polymerases arerandomly or semi-randomly shuffled via available gene shufflingtechniques (e.g., via “family gene shuffling”; see Crameri et al. (1998)“DNA shuffling of a family of genes from diverse species acceleratesdirected evolution” Nature 391:288-291; Clackson et al. (1991) “Makingantibody fragments using phage display libraries” Nature 352:624-628;Gibbs et al. (2001) “Degenerate oligonucleotide gene shuffling (DOGS): amethod for enhancing the frequency of recombination with familyshuffling” Gene 271:13-20; and Hiraga and Arnold (2003) “General methodfor sequence-independent site-directed chimeragenesis: J. Mol. Biol.330:287-296). In these methods, the recombination points can bepredetermined such that the gene fragments assemble in the correctorder. However, the combinations, e.g., chimeras, can be formed atrandom. For example, using methods described in Clarkson et al., fivegene chimeras, e.g., comprising segments of a Phi29 polymerase, a PZApolymerase, an M2 polymerase, a B103 polymerase, and a GA-1 polymerase,can be generated. Appropriate mutations to improve branching fraction,increase closed complex stability, or alter reaction rate constants canbe introduced into the chimeras.

Available DNA polymerase enzymes have also been modified in any of avariety of ways, e.g., to reduce or eliminate exonuclease activities(many native DNA polymerases have a proof-reading exonuclease functionthat interferes with, e.g., sequencing applications), to simplifyproduction by making protease digested enzyme fragments such as theKlenow fragment recombinant, etc. As noted, polymerases have also beenmodified to confer improvements in specificity, processivity, andimproved retention time of labeled nucleotides inpolymerase-DNA-nucleotide complexes (e.g., WO 2007/076057 PolymerasesFor Nucleotide Analogue Incorporation by Hanzel et al. and WO2008/051530 Polymerase Enzymes And Reagents For Enhanced Nucleic AcidSequencing by Rank et al.), to alter branch fraction and translocation(e.g., US Pub. No. 20100075332 entitled “Engineering Polymerases AndReaction Conditions For Modified Incorporation Properties”), to increasephotostability (e.g., US Pub. No. 20100093555 entitled “EnzymesResistant to Photodamage”), and to improve surface-immobilized enzymeactivities (e.g., WO 2007/075987 Active Surface Coupled Polymerases byHanzel et al. and WO 2007/076057 Protein Engineering Strategies ToOptimize Activity Of Surface Attached Proteins by Hanzel et al.). Insome cases, the polymerase is modified in order to more effectivelyincorporate desired nucleotide analogs, e.g. analogs having four or morephosphates in their polyphosphate chain. Enzymes mutated to more readilyaccept nucleotide analogs having such properties are described, forexample in the applications described above and in US20120034602—Recombinant Polymerases for Improved Single MoleculeSequencing; US 20100093555—Enzymes Resistant to Photodamage; US20110189659—Generation of Modified Polymerases for Improved Accuracy inSingle Molecule Sequencing; US 20100112645—Generation of ModifiedPolymerases for Improved Accuracy in Single Molecule Sequencing; US2008/0108082—Polymerase enzymes and reagents for enhanced nucleic acidsequencing; and US 20110059505—Polymerases for Nucleotide AnalogueIncorporation which are incorporated herein by reference in theirentirety for all purposes.

Many polymerases that are suitable for modification are available, e.g.,for use in sequencing, labeling and amplification technologies. Forexample, human DNA Polymerase Beta is available from R&D systems. DNApolymerase I is available from Epicenter, GE Health Care, Invitrogen,New England Biolabs, Promega, Roche Applied Science, Sigma Aldrich andmany others. The Klenow fragment of DNA Polymerase I is available inboth recombinant and protease digested versions, from, e.g., Ambion,Chimerx, eEnzyme LLC, GE Health Care, Invitrogen, New England Biolabs,Promega, Roche Applied Science, Sigma Aldrich and many others. ϕ29 DNApolymerase is available from e.g., Epicentre. Poly A polymerase, reversetranscriptase, Sequenase, SP6 DNA polymerase, T4 DNA polymerase, T7 DNApolymerase, and a variety of thermostable DNA polymerases (Taq, hotstart, titanium Taq, etc.) are available from a variety of these andother sources. Recent commercial DNA polymerases include Phusion™High-Fidelity DNA Polymerase, available from New England Biolabs; GoTaq®Flexi DNA Polymerase, available from Promega; RepliPHI™ ϕ29 DNAPolymerase, available from Epicentre Biotechnologies; PfuUltra™ HotstartDNA Polymerase, available from Stratagene; KOD HiFi DNA Polymerase,available from Novagen; and many others. Biocompare(dot)com providescomparisons of many different commercially available polymerases.

DNA polymerases that are preferred substrates for mutation to improvedesired properties (e.g., for use in single molecule sequencing,include, e.g. Taq polymerases, exonuclease deficient Taq polymerases, E.coli DNA Polymerase 1, Klenow fragment, reverse transcriptases,ϕ29-related polymerases including wild type ϕ29 polymerase andderivatives of such polymerases such as exonuclease deficient forms, T7DNA polymerase, T5 DNA polymerase, an RB69 polymerase, etc.

In one aspect, the polymerase of use in the methods and compositionsdescribed herein is a modified ϕ29-type DNA polymerase. For example, themodified recombinant DNA polymerase can be homologous to a wild-type orexonuclease deficient ϕ29 DNA polymerase, e.g., as described in U.S.Pat. Nos. 5,001,050, 5,198,543, or 5,576,204. Alternately, the modifiedrecombinant DNA polymerase can be homologous to other ϕ29-type DNApolymerases, such as B103, GA-1, PZA, ϕ15, BS32, M2Y, Nf, G1, Cp-1,PRD1, PZE, SFS, Cp-5, Cp-7, PR4, PR5, PR722, L17, ϕ21, or the like. Fornomenclature, see also, Meijer et al. (2001) “ϕ29 Family of Phages”Microbiology and Molecular Biology Reviews, 65(2):261-287. Suitablepolymerases are described, for example, in U.S. Patent applicationpublications 2007-0196846, 2008-0108082, 2010-0075332, 2010-0093555,2010-0112645, 2011-0189659, 2012-0034602, 2013-0217007, 2014-0094374,and 2014-0094375.

In further embodiments, the polymerase enzyme used in the methods of theinvention includes RNA dependent DNA polymerases or reversetranscriptases. Suitable reverse transcriptase enzymes include HIV-1,M-MLV, AMV, and Telomere Reverse Transcriptase. Reverse transcriptasesalso allow for the direct sequencing of RNA substrates such as messengerRNA, transfer RNA, non-coding RNA, ribosomal RNA, micro RNA or catalyticRNA.

The polymerase enzymes of use in the present invention generally requirea primer. While in most cases an oligonucleotide primer is used, in somecases a protein such as a terminal protein can act as a primer. In otherembodiments, self-priming templates are employed. Oligonucleotideprimers are generally complementary to a portion of the template nucleicacid. The primers can comprise naturally occurring RNA or DNAoligonucleotides. The primers may also be synthetic analogs. The primersmay have alternative backbones as described above for the nucleic acidsof the invention. The primer may also have other modifications, such asthe inclusion of heteroatoms, the attachment of labels, such as dyes, orsubstitution with functional groups which will still allow for basepairing and for recognition by the enzyme. Primers can select tighterbinding primer sequences, e.g., GC rich sequences, as well as employprimers that include within their structure non-natural nucleotides ornucleotide analogs, e.g., peptide nucleic acids (PNAs) or locked nucleicacids (LNAs), that can demonstrate higher affinity pairing with thetemplate. The primer can also be selected to influence the kinetics ofthe polymerase reaction.

To reduce or prevent undesired dissociation of the polymerase from thetemplate and primer, the processivity of the polymerase can be increasedby locking the template in place in the enzyme, e.g., with chemicalcross-links. For example, a bifunctional cross-linker can be reactedwith residues in the polymerase on each side of the bound template,topologically encircling the template. See, e.g., U.S. Pat. No.7,745,116 and US patent application publication 2015/0086994, each ofwhich is incorporated herein by reference in its entirety for allpurposes. Cysteine residues can be introduced into the polymerase atsuitable positions for cross-link formation. For example, a recombinantϕ29 polymerase can include, e.g., A83C and E420C substitutions, D84C andE418C substitutions, V19C and N409C substitutions, and/or N409C andV568C substitutions. (See, e.g., US patent application publication2014/0094375, incorporated herein by reference in its entirety for allpurposes, for the sequence of wild-type ϕ29 polymerase.) Existingsolvent accessible cysteine residues can be mutated to ensure that thecross-link is formed between the desired pair of residues; thus, asuitable recombinant ϕ29 polymerase can also include one or moresubstitutions such as, e.g., C106S and/or C448V. Suitable bifunctionallinkers are known in the art, for example, a bismaleimide linker, e.g.,a bismaleimide-PEG linker, e.g., 1,11-bismaleimido-triethyleneglycol(BM(PEG)₃). Other coupling chemistries that can be employed include,e.g., thiol reactive reagents and disulfide containing reagents, e.g.,haloacetyl crosslinkers (e.g., linkers including twoiodoacetyl/iodoacetamide or bromoacetyl groups) and linkers with twopyridyl disulfide groups. The body of the linker can include, e.g., PEG(polyethylene glycol), an oligopeptide (e.g., polyglycine), or the like.Optimal linker length can be chosen based on the distance between thetwo residues to be cross-linked, e.g., in a crystal structure or othermodel of the polymerase. The linker is typically reacted with thepolymerase after binding of the template (or primer/template); suitablereaction conditions for various linker chemistries are known in the art.Noncovalent linkers can also be employed. Such topological encirclementof the template by polymerase can be particularly effective for circulartemplates (including, e.g., simple circles and SMRTbells™ as describedin, e.g., U.S. Pat. No. 8,153,375 “Compositions and Methods for NucleicAcid Sequencing” and Travers et al. (2010) Nucl. Acids Res. 38(15):e159,each of which is incorporated herein by reference in its entirety forall purposes).

Many native DNA polymerases have a proof-reading exonuclease functionwhich can yield substantial data analysis problems in processes thatutilize real time observation of incorporation events as a method ofidentifying sequence information, e.g., single molecule sequencingapplications. Even where exonuclease activity does not introduce suchproblems in single molecule sequencing, reduction of exonucleaseactivity can be desirable since it can increase accuracy (in some casesat the expense of readlength).

Accordingly, polymerases for use in the above techniques optionallyinclude one or more mutations (e.g., substitutions, insertions, and/ordeletions) relative to the parental polymerase that reduce or eliminateendogenous exonuclease activity. For example, relative to wild-type ϕ29DNA polymerase, one or more of positions N62, D12, E14, T15, H61, D66,D169, K143, Y148, and H149 is optionally mutated to reduce exonucleaseactivity in a recombinant ϕ29 polymerase. Exemplary mutations that canreduce exonuclease activity in a recombinant ϕ29 polymerase include,e.g., N62D, N62H, D12A, T151, E14I, E14A, D66A, K143D, D145A and D169Asubstitutions, as well as addition of an exogenous feature at theC-terminus (e.g., a polyhistidine tag). See, e.g., US patent applicationpublication 2014/0094375, incorporated herein by reference in itsentirety for all purposes, for the sequence of wild-type ϕ29 polymerase.

IX. Applications for Methods and Compositions of the Invention:Sequencing

The methods, devices, and compositions of the invention are particularlyuseful for single molecule sequencing methods, and specifically singlemolecule sequencing by incorporation in real time, because the presentinvention provides a way to efficiently load reaction regions occupiedby a single polymerase composition. In general, the high density singlemolecule loading achieved by methods and compositions described hereinallow single molecule analysis to be conducted more efficiently and withgreater speed, because there will be fewer “unusable” regions on asubstrate surface for the sequencing reaction (i.e., regions that haveno or multiple polymerase compositions loaded, which provide either noinformation (for the empty regions) or sequencing information that mustbe deconvoluted to account for the multiply loaded molecules).

In some aspects, the present invention includes methods of analyzing thesequence of template nucleic acids associated with the polymerasecompositions described herein. In such aspects, the sequence analysisemploys template dependent synthesis in identifying the nucleotidesequence of the template nucleic acid. Nucleic acid sequence analysisthat employs template dependent synthesis identifies individual bases,or groups of bases, as they are added during a template mediatedsynthesis reaction, such as a primer extension reaction, where theidentity of the base is required to be complementary to the templatesequence to which the primer sequence is hybridized during synthesis.Other such processes include ligation driven processes, where oligo- orpolynucleotides are complexed with an underlying template sequence, inorder to identify the sequence of nucleotides in that sequence.Typically, such processes are enzymatically mediated using nucleic acidpolymerases, such as DNA polymerases, RNA polymerases, reversetranscriptases, and the like, or other enzymes such as in the case ofligation driven processes, e.g., ligases.

Sequence analysis using template dependent synthesis can include anumber of different processes. For example, in embodiments utilizingsequence by synthesis processes, individual nucleotides or nucleotideanalogs are identified iteratively as they are added to the growingprimer extension product.

For sequencing processes that rely upon monitoring of the incorporationof nucleotides into growing nascent strands being synthesized by thecomplex, the progress of the reaction through these steps can ofsignificant importance. In particular, for certain “real-time”nucleotide incorporation monitoring processes, the detectability of theincorporation event is improved based upon the amount of time thenucleotide is incorporated into and retained within the synthesiscomplex during its ultimate incorporation into a primer extensionproduct. By way of example, in certain exemplary processes, the presenceof the nucleotide in the synthesis complex is detected either by virtueof a focused observation of the synthesis complex, or through the use ofinteractive labeling techniques that produce characteristic signals whenthe nucleotide is within the synthesis complex. See, e.g., Levene, etal., Science 299:682-686, January 2003, and Eid, J. et al., Science,323(5910), 133-138 (2009), the full disclosures of which areincorporated herein by reference in their entirety for all purposes.

In further aspects, the methods of the present invention include stepsfrom any single molecule sequencing methods known in the art. See, e.g.,Rigler, et al., DNA-Sequencing at the Single Molecule Level, Journal ofBiotechnology, 86(3): 161 (2001); Goodwin, P. M., et al., Application ofSingle Molecule Detection to DNA Sequencing. Nucleosides & Nucleotides,16(5-6): 543-550 (1997); Howorka, S., et al., Sequence-SpecificDetection of Individual DNA Strands using Engineered Nanopores, NatureBiotechnology, 19(7): 636-639 (2001); Meller, A., et al., Rapid NanoporeDiscrimination Between Single Polynucleotide Molecules, Proceedings ofthe National Academy of Sciences of the United States of America, 97(3):1079-1084 (2000); Driscoll, R. J., et al., Atomic-Scale Imaging of DNAUsing Scanning Tunneling Microscopy. Nature, 346(6281): 294-296 (1990).

In further embodiments, methods of single molecule sequencing known inthe art include detecting individual nucleotides as they areincorporated into a primed template, i.e., sequencing by synthesis. Suchmethods often utilize exonucleases to sequentially release individualfluorescently labeled bases as a second step after DNA polymerase hasformed a complete complementary strand. See Goodwin et al., “Applicationof Single Molecule Detection to DNA Sequencing,” Nucleos. Nucleot. 16:543-550 (1997).

In general, for sequencing methods utilizing compositions of the presentinvention, individual polymerase compositions are provided withinseparate discrete regions of a support. For example, in some cases,individual complexes may be provided within individual confinementstructures, including nanoscale structures such as nanoscale wells. Infurther examples, zero-mode waveguide cores or any of the reactionchambers discussed above in the stepwise sequencing section serve as thereaction regions for sequencing methods utilizing compositions of thepresent invention. Examples of waveguides and processes for immobilizingindividual complexes therein are described in, e.g., PublishedInternational Patent Application No. WO 2007/123763, the full disclosureof which is incorporated herein by reference in its entirety for allpurposes and in particular for all teachings related to providingindividual complexes into individual confinement structures. In somecases the molecules of interest (e.g., polymerase/template complexes)can be provided onto or proximal to structures or regions that allow forelectronic single molecule sequencing. Such structures can includenanoscale electronic structures such as electrodes, capacitors, or fieldeffect transducers (nanoFETs). NanoFETs include those having carbonnanotube gates. Such structures and their use for single moleculesequencing are described, for example, in U.S. Patent ApplicationPublication No. 2015/0065353 which is incorporated herein in itsentirety for all purposes and in particular for all teachings related tostructures for use in single molecule sequencing.

Incorporation of labeled nucleotide analogs by polymerases isparticularly useful in a variety of different nucleic acid analyses,including real-time monitoring of DNA polymerization. The label canitself be incorporated, or more preferably, can be released duringincorporation of the analog. For example, analog incorporation can bemonitored in real time by monitoring label release during incorporationof the analog by the polymerase. The portion of the analog that isincorporated can be the same as a natural nucleotide, or can includefeatures of the analog that differ from a natural nucleotide.

In general, label incorporation or release can be used to indicate thepresence and composition of a growing nucleic acid strand, e.g.,providing evidence of template replication/amplification and/or sequenceof the template. Signaling from the incorporation can be the result ofdetecting labeling groups that are liberated from the incorporatedanalog, e.g., in a solid phase assay, or can arise upon theincorporation reaction. For example, in the case of FRET labels where abound label is quenched and a free label is not, release of a labelgroup from the incorporated analog can give rise to a fluorescentsignal. Alternatively, the enzyme may be labeled with one member of aFRET pair proximal to the active site, and incorporation of an analogbearing the other member will allow energy transfer upon incorporation.The use of enzyme bound FRET components in nucleic acid sequencingapplications is described, e.g., in U.S. Patent Application PublicationNo. 2003/0044781, incorporated herein by reference.

In one example reaction of interest, a polymerase reaction can beisolated within an extremely small observation volume that effectivelyresults in observation of individual polymerase molecules. As a result,the incorporation event provides observation of an incorporatingnucleotide analog that is readily distinguishable from non-incorporatednucleotide analogs. In a preferred aspect, such small observationvolumes are provided by immobilizing the polymerase enzyme within anoptical confinement, such as a Zero Mode Waveguide (ZMW). For adescription of ZMWs and their application in single molecule analyses,and particularly nucleic acid sequencing, see, e.g., U.S. PatentApplication Publication No. 2003/0044781 and U.S. Pat. No. 6,917,726,each of which is incorporated herein by reference in its entirety forall purposes. See also Levene et al. (2003) “Zero-mode waveguides forsingle-molecule analysis at high concentrations” Science 299:682-686,Eid et al. (2009) “Real-time DNA sequencing from single polymerasemolecules” Science 323:133-138, and U.S. Pat. Nos. 7,056,676, 7,056,661,7,052,847, and 7,033,764, the full disclosures of which are incorporatedherein by reference in their entirety for all purposes.

In general, a polymerase enzyme is complexed with the template strand inthe presence of one or more nucleotides and/or one or more nucleotideanalogs. For example, in certain embodiments, labeled analogs arepresent representing analogous compounds to each of the four naturalnucleotides, A, T, G and C, e.g., in separate polymerase reactions, asin classical Sanger sequencing, or multiplexed together, e.g., in asingle reaction, as in multiplexed sequencing approaches. When aparticular base in the template strand is encountered by the polymeraseduring the polymerization reaction, it complexes with an availableanalog that is complementary to such nucleotide, and incorporates thatanalog into the nascent and growing nucleic acid strand. In one aspect,incorporation can result in a label being released, e.g., inpolyphosphate analogs, cleaving between the α and β phosphorus atoms inthe analog, and consequently releasing the labeling group (or a portionthereof). The incorporation event is detected, either by virtue of alonger presence of the analog and, thus, the label, in the complex, orby virtue of release of the label group into the surrounding medium.Where different labeling groups are used for each of the types ofanalogs, e.g., A, T, G or C, identification of a label of anincorporated analog allows identification of that analog andconsequently, determination of the complementary nucleotide in thetemplate strand being processed at that time. Sequential reaction andmonitoring permits real-time monitoring of the polymerization reactionand determination of the sequence of the template nucleic acid. As notedabove, in particularly preferred aspects, the polymerase enzyme/templatecomplex is provided immobilized within an optical confinement thatpermits observation of an individual complex, e.g., a zero modewaveguide. For additional information on single molecule sequencingmonitoring incorporation of phosphate-labeled analogs in real time, see,e.g., Eid et al. (2009) “Real-time DNA sequencing from single polymerasemolecules” Science 323:133-138.

In a first exemplary technique, a nucleic acid synthesis complex,including a polymerase enzyme, a template sequence and a complementaryprimer sequence, is provided immobilized within an observation regionthat permits illumination and observation of a small volume thatincludes the complex without excessive illumination of the surroundingvolume. By illuminating and observing only the volume immediatelysurrounding the complex, one can readily identify fluorescently labelednucleotides that become incorporated during that synthesis, as suchnucleotides are retained within that observation volume by thepolymerase for longer periods than those nucleotides that are simplyrandomly diffusing into and out of that volume. In particular, when anucleotide is incorporated into DNA by the polymerase, it is retainedwithin the observation volume for a prolonged period of time, and uponcontinued illumination yields a prolonged fluorescent signal. Bycomparison, randomly diffusing and not incorporated nucleotides remainwithin the observation volume for much shorter periods of time, and thusproduce only transient signals, many of which go undetected due to theirextremely short duration.

In particularly preferred exemplary systems, the confined illuminationvolume is provided through the use of arrays of optically confinedapertures termed zero mode waveguides (ZMWs). See, e.g., U.S. Pat. No.6,917,726, which is incorporated herein by reference in its entirety forall purposes. For sequencing applications, the DNA polymerase istypically provided immobilized upon the bottom of the ZMW, althoughanother component of the complex (e.g., a primer or template) isoptionally immobilized on the bottom of the ZMW to localize the complex.See, e.g., Korlach et al. (2008) PNAS U.S.A. 105(4):1176-1181 and USpatent application publication 2008-0032301, each of which isincorporated herein by reference in its entirety for all purposes.

In operation, the fluorescently labeled nucleotides (e.g., analogscorresponding to A, C, G and T) bear one or more fluorescent dye groupson a terminal phosphate moiety that is cleaved from the nucleotide uponincorporation. As a result, synthesized nucleic acids do not bear thebuild-up of fluorescent labels, as the labeled polyphosphate groupsdiffuse away from the complex following incorporation of the associatednucleotide, nor do such labels interfere with the incorporation event.See, e.g., Korlach et al. (2008) Nucleosides, Nucleotides and NucleicAcids 27:1072-1083.

In a second exemplary technique, the immobilized complex and thenucleotides to be incorporated are each provided with interactivelabeling components. Upon incorporation, the nucleotide borne labelingcomponent is brought into sufficient proximity to the complex borne (orcomplex proximal) labeling component, such that these components producea characteristic signal event. For example, the polymerase may beprovided with a fluorophore that provides fluorescent resonant energytransfer (FRET) to appropriate acceptor fluorophores. These acceptorfluorophores are provided upon the nucleotide to be incorporated, whereeach type of nucleotide bears a different acceptor fluorophore, e.g.,that provides a different fluorescent signal. Upon incorporation, thedonor and acceptor are brought close enough together to generate energytransfer signal. By providing different acceptor labels on the differenttypes of nucleotides, one obtains a characteristic FRET-basedfluorescent signal for the incorporation of each type of nucleotide, asthe incorporation is occurring.

In a related aspect, a nucleotide analog may include two interactingfluorophores that operate as a donor/quencher pair, where one member ispresent on the nucleobase or other retained portion of the nucleotide,while the other member is present on a phosphate group or other portionof the nucleotide that is released upon incorporation, e.g., a terminalphosphate group. Prior to incorporation, the donor and quencher aresufficiently proximal on the same analog as to provide characteristicsignal quenching. Upon incorporation and cleavage of the terminalphosphate groups, e.g., bearing a donor fluorophore, the quenching isremoved and the resulting characteristic fluorescent signal of the donoris observable.

In exploiting the foregoing processes, where the incorporation reactionoccurs too rapidly, it may result in the incorporation event not beingdetected, i.e., the event speed exceeds the detection speed of themonitoring system. The missed detection of incorporated nucleotides canlead to an increased rate of errors in sequence determination, asomissions in the real sequence. In order to mitigate the potential formissed pulses due to short reaction or product release times, in oneaspect, the current invention can result in increased reaction and/orproduct release times during incorporation cycles. Similarly, very shortinterpulse distances can occasionally cause pulse merging. An advantageof employing polymerases with reduced reaction rates, e.g., polymerasesexhibiting decreased rates and/or two slow-step kinetics as described inUS patent application publications 2009-0286245 and 2010-0112645, is anincreased frequency of longer, detectable, binding events. Thisadvantage may also be seen as an increased ratio of longer, detectablepulses to shorter, non-detectable pulses, where the pulses representbinding events.

The sequencing processes, e.g., using the substrates described above andthe compositions of the invention, are generally exploited in thecontext of a fluorescence optical system that is capable of illuminatingthe various complexes on the substrate, and obtaining, detecting andseparately recording fluorescent signals from these complexes. Suchsystems typically employ one or more illumination sources that provideexcitation light of appropriate wavelength(s) for the labels being used.An optical train directs the excitation light at the reaction region(s)and collects emitted fluorescent signals and directs them to anappropriate detector or detectors. Additional components of the opticaltrain can provide for separation of spectrally different signals, e.g.,from different fluorescent labels, and direction of these separatedsignals to different portions of a single detector or to differentdetectors. Other components may provide for spatial filtering of opticalsignals, focusing and direction of the excitation and or emission lightto and from the substrate. An exemplary system is also described inLundquist et al., Published U.S. Patent Application No. 2007-0036511,Optics Letters, Vol. 33, Issue 9, pp. 1026-1028, the full disclosure ofwhich is incorporated herein by reference in its entirety for allpurposes.

Fluorescence reflective optical trains can be used in the applicationsof the systems of the invention. For a discussion on the advantages ofsuch systems, see, e.g., U.S. patent application Ser. No. 11/704,689,filed Feb. 9, 2007, Ser. No. 11/483,413, filed Jul. 7, 2006, and Ser.No. 11/704,733, filed Feb. 9, 2007, the full disclosures of which areincorporated herein by reference in their entirety for all purposes.

In the context of the nucleic acid sequencing methods described herein,it will be appreciated that the signal sources each represent sequencingreactions, and particularly, polymerase mediated, template dependentprimer extension reactions, where in preferred aspects, each baseincorporation event results in a prolonged illumination (orlocalization) of one of four differentially labeled nucleotides beingincorporated, so as to yield a recognizable pulse (peak) that carries adistinguishable spectral profile or color.

In further embodiments, compositions of the present invention areutilized in sequencing methods utilizing nanopores. In exemplaryembodiments, enzymes are loaded into a nanopore—the nanopore comprisesbinding moieties complementary to reaction moieties on the enzyme (oranother molecule associated with the enzyme, e.g., a template). In thisway, a single enzyme is loaded into each nanopore. In certainembodiments, the enzymes are attached proximal to the nanopore. As willbe appreciated, helicases and exonucleases as well as polymerases can beused in nanopore sequencing and can be loaded by the techniquesdescribed herein. Methods of nanopore sequencing are known in the artand disclosed for example in US Published App. Nos. 2013/0327644 and2014/0051068, which are hereby incorporated by reference for allpurposes and in particular for all teachings, written description,figures and figure legends related to nanopore sequencing.

The present invention can further include computer implementedprocesses, and/or software incorporated onto a computer readable mediuminstructing such processes, as set forth in greater detail below. Assuch, signal data generated by the reactions and optical systemsdescribed above, is input or otherwise received into a computer or otherdata processor, and subjected to one or more of the various processsteps or components set forth below. Once these processes are carriedout, the resulting output of the computer implemented processes may beproduced in a tangible or observable format, e.g., printed in a userreadable report, displayed upon a computer display, or it may be storedin one or more databases for later evaluation, processing, reporting orthe like, or it may be retained by the computer or transmitted to adifferent computer for use in configuring subsequent reactions or dataprocesses.

Computers for use in carrying out the processes of the invention canrange from personal computers such as PC or Macintosh® type computersrunning Intel Pentium or DuoCore processors, to workstations, laboratoryequipment, or high speed servers, running UNIX, LINUX, Windows®, orother systems. Logic processing of the invention may be performedentirely by general purposes logic processors (such as CPU's) executingsoftware and/or firmware logic instructions; or entirely by specialpurposes logic processing circuits (such as ASICs) incorporated intolaboratory or diagnostic systems or camera systems which may alsoinclude software or firmware elements; or by a combination of generalpurpose and special purpose logic circuits. Data formats for the signaldata may comprise any convenient format, including digital image baseddata formats, such as JPEG, GIF, BMP, TIFF, or other convenient formats,while video based formats, such as avi, mpeg, mov, rmv, or other videoformats may be employed. The software processes of the invention maygenerally be programmed in a variety of programming languages including,e.g., Matlab, C, C++, C#, NET, Visual Basic, Python, JAVA, CGI, and thelike.

In some cases, the compositions, methods, and systems of the inventioncan be used as part of an integrated sequencing system, for example, asdescribed in US 20120014837—Illumination of Integrated AnalyticalSystems, US 20120021525—Optics Collection and Detection System andMethod, US 20120019828—Integrated Analytical System and Method,61/660,776 filed Jun. 17, 2012—Arrays of Integrated Analytical Devicesand Methods for Production, and US 20120085894—Substrates and OpticalSystems and Methods of Use Thereof which are incorporated herein byreference in their entirety for all purposes.

In certain embodiments, the sequencing compositions described hereinwill be provided in whole, or in part, in kit form enabling one to carryout the processes described herein. Such kits will typically compriseone or more components of the reaction complex, such as the polymeraseenzyme and primer sequences. Such kits will also typically includebuffers and reagents for loading of the polymerase and/or a template asin the processes described herein. The kits will also optionally includeother components for carrying out sequencing applications in accordancewith those methods described herein. In particular, such kits mayinclude ZMW array substrates for use in observing individual reactioncomplexes as described herein.

In addition to the various components set forth above, the kits willtypically include instructions for combining the various components inthe amounts and/or ratios set forth herein, to carry out the desiredprocesses, as also described or referenced herein, e.g., for performingsequence by incorporation reactions.

X. Substrates and Surfaces

Substrates of use in particular sequencing methods of the invention areknown in the art and discussed herein, and as will be appreciated, anyof the substrates discussed herein can be used in any combination forany embodiments discussed herein.

In exemplary embodiments, methods of sequencing of the invention utilizesubstrates that include one or more reaction regions (also referred toherein as “reaction chambers” and “array regions”) arranged in the formof an array on an inert substrate material, also referred to herein as a“solid support” or “surface”, that allows for combination of thereactants in a sequencing reaction in a defined space and for detectionof the sequencing reaction event. A reaction region can be a localizedarea on the substrate material that facilitates interaction ofreactants, e.g., in a nucleic acid sequencing reaction. A reactionregion may in certain embodiments be a nanoscale well (also referred toherein as a nanowell), and in further embodiments the nanowell is a ZMW.A nanoscale well typically has dimensions in the nanometer range, i.e.,less than 1 micrometer. In some embodiments, a nanoscale well has across-sectional diameter of less than 1000, 900, 800, 700, 600, or 500nm, e.g., less than 400, 350, 300, 250, or 200 nm. In some embodiments,a nanoscale well has a depth of less than 1000, 900, 800, 700, 600, or500 nm, e.g., less than 400, 350, 300, 250, or 200 nm. As discussedherein, the sequencing reactions contemplated by the invention can insome embodiments occur on numerous individual nucleic acid samples intandem, in particular simultaneously sequencing numerous nucleic acidsamples, e.g., derived from genomic and chromosomal DNA. The apparatusof the invention can therefore include an array having a sufficientnumber of array regions/reaction regions to carry out such numerousindividual sequencing reactions. In one embodiment, the array comprisesat least 1,000 reaction regions. In another embodiment, the arraycomprises greater than 400,000 reaction regions, preferably between400,000 and 20,000,000 reaction regions. In a more preferred embodiment,the array comprises between 1,000,000 and 16,000,000 reaction regions,e.g., 1,000,000, 2,000,000, 3,000,000, 4,000,000, 5,000,000, 6,000,000,7,000,000, 8,000,000, 9,000,000, or 10,000,000 reaction regions.

The reaction regions on the array may take the form of a cavity or wellin the substrate material, having a width and depth, into whichreactants can be deposited. One or more of the reactants typically arebound to the substrate material in the reaction region and the remainderof the reactants are in a medium which facilitates the reaction andwhich flows through or contacts the reaction region. When formed ascavities or wells, the chambers are preferably of sufficient dimensionand order to allow for (i) the introduction of the necessary reactantsinto the chambers, (ii) reactions to take place within the chamber and(iii) inhibition of mixing of reactants between chambers. The shape ofthe well or cavity is preferably circular or cylindrical, but can bemultisided so as to approximate a circular or cylindrical shape. Inanother embodiment, the shape of the well or cavity is substantiallyhexagonal. The cavity can have a smooth wall surface. In an additionalembodiment, the cavity can have at least one irregular wall surface. Thecavities can have, e.g, a planar bottom or a concave bottom.

The reaction regions may in some situations take the form of a nanopore.Such reaction regions, including arrays of nanopores, are known in theart and described for example in US Published App. Nos. 2013/0327644 and2014/0051068, which are hereby incorporated by reference in theirentirety for all purposes and in particular for all teachings related tonanopore arrays.

Any material can be used as the solid support material, as long as thesurface allows for stable attachment of polymerase enzyme complexes andoptionally detection of nucleotide incorporation. The solid supportmaterial can be planar or can be cavitated, e.g., in a cavitatedterminus of a fiber optic or in a microwell etched, molded, or otherwisemicromachined into the planar surface, e.g. using techniques commonlyused in the construction of microelectromechanical systems. See e.g.,Rai-Choudhury, HANDBOOK OF MICROLITHOGRAPHY, MICROMACHINING, ANDMICROFABRICATION, VOLUME 1: MICROLITHOGRAPHY, Volume PM39, SPIE Press(1997); Madou, CRC Press (1997), Aoki, Biotech. Histochem. 67: 98-9(1992); Kane et al., Biomaterials. 20: 2363-76 (1999); Deng et al.,Anal. Chem. 72:3176-80 (2000); Zhu et al., Nat. Genet. 26:283-9 (2000).In some embodiments, the solid support is optically transparent, e.g.,glass.

Suitable substrates include chips having arrays of nanoscale wells orzero mode waveguides. Exemplary substrates include substrates having ametal or metal oxide layer on a silica-based layer, with nanoscale wellsdisposed through the metal or metal layer to or into the silica-basedlayer. Such substrates are described, for example in U.S. patentapplication Ser. Nos. 10/259,268, 14/187,198, 14/107,730, 13/920,037,and U.S. Pat. Nos. 8,994,946, 8,906,670, 8,993,307, 8,802,600,7,907,800, and 7,302,146, which are incorporated herein by reference intheir entirety for all purposes and in particular for all teachingsrelated to substrates.

EXAMPLES Example 1: Preparing Tethered Nucleic Acid Reagent for Use inHelix Drive Methods

An exemplary route for preparing a tethered nucleic acid for use in thehelix drive methods described herein is provided in FIG. 14 . Aspictured in FIG. 14 , two DNA fragments that are mirror images of eachother (i.e., the top strand of 1401 is identical to the bottom strand of1402) are subjected to PCR amplification. 1401 has a biotin containingcapture moiety (1403) added to the 5′ end of one strand through the PCRreaction. The resultant products are then subjected to restrictionendonuclease digestion to create overhangs that are complementary toadaptor 1404. Sticky end ligation joins the two fragments, creating adouble stranded nucleic acid where each strand containsself-complementary regions (i.e., region 1405 and 1406 of the top strandare complementary to each other). A terminal transferase reaction adds addNTP-azido group to the 3′ end of both strands, which can allow forfurther attachment of moieties for surface attachment. For example,biotin (or another means of immobilizing the tethering nucleic acid on asurface) can be attached via reaction with the azido group. Afterimmobilization of the tether at a desired site and capture of a moleculeof interest, the lower strand can then be digested by T7 exonuclease,which has 5′ to 3′ dsDNA exonuclease activity, leaving the top strandand its capture moiety (and anything that may be attached to the capturemoiety, such as a molecule of interest) intact. The two complementaryregions 1405 and 1406 would then be free to hybridize to each other todraw the nucleic acid 1408 into a hairpin shape as described in furtherdetail herein.

Another exemplary route for preparing a tethered nucleic acid for use inhelix drive methods is provided in FIG. 15 . This route produces apartially double stranded, partially single stranded construct thatcontains long inverted repeat sequences. Starting with the circularconstruct 1501, the double stranded portion has complementary strands1502 and 1503. A nick 1504 generated using methods known in the art,including a site-specific nickase or a lyase, results in the circularconstruct becoming a linear construct that is then replicated for oneround (1505) to produce duplex 1506 that now contains an invertedrepeat. Optionally, this round of replication is performed with dUTPsuch that the product strand can be digested later with UDG (uracil-DNAglycosylase) and endonuclease VIII. An adapter 1507 can optionally beligated to the end of the duplex to produce the double strandedtethering nucleic acid reagent for use in helix drive methods describedherein. It will be evident that although adapter 1507 as shown in FIG.15 is a hairpin, an adapter having a 5′ or 3′ overhang or blunt ends canalso be employed.

As noted, one technique for removing one strand of the double strandedtethering nucleic acid is to incorporate uracil into that strand.Another exemplary technique for removing one strand of the doublestranded tethering nucleic acid employs an exonuclease. In this example,construct 1501 includes an exonuclease resistant moiety (e.g., one ormore phosphorothioate linkages or a biotin moiety), e.g., in loop 1511.Adapter 1507 can in such an example be a hairpin adapter that includes anick site; in other embodiments, instead of being a hairpin the adapteris a linear adapter having a free end such that it is subject toexonuclease degradation. (The adapter optionally includes a biotin orother immobilization moiety, e.g., on the other terminus of a linearadapter.) A suitable exonuclease is then employed to digest one strand,starting at the nick in hairpin adapter 1507 or at its free end inembodiments where it is a linear adapter; the exonuclease resistantmoiety in loop 1511 can then halt the exonuclease and protect the otherstrand from degradation.

A further method for creating a tethering nucleic acid moleculecontaining long inverted repeats for use in helix drive methods is tocreate a long RNA strand that is self-complementary via transcriptionwith a phage polymerase. Long inverted repeats can be difficult to cloneinto bacteria, and this method thus provides a way to manufacturenucleic acids, particularly DNA/RNA hybrids, containing such longinverted repeats at scale in a test tube. FIG. 16 shows a method inwhich two separate PCR reactions are performed to create the sameapproximate product but with T7 and SP6 bacteriophage promoters onopposite ends. The exemplary embodiment shown in FIG. 16 is for creationof a 1 kb RNA/DNA hybrid. The phage polymerases allow the production ofa large amount of 50-1000 nt RNA and the short (˜20 nt) promotersequence can be appended onto the 5′ end of an oligonucleotide duringstandard phosphoramidite synthesis. PCR with Taq DNA polymerasesynthesis toward the polylinker sequence of pUC18 plasmid (or any othergeneric non-organismal sequence) is performed. The amplificationproducts can be joined tail to tail to create one transcription cassettefor RNA production. In the exemplary embodiment of FIG. 16 , the first500 nt of the RNA is complementary to the 2nd 500 nt. Possible joiningstrategies include (1) phosphorylation on only one end of each PCRproduct and then blunt ligation or (2) incorporation of a sticky endrestriction site in the PCR primers so that cutting and stitchingtogether is more favorable. In this second method, it may be useful touse non-palindromic sites so that only the correct linkage of product1+product 2 can form. For either 1 or 2, it can also be beneficial touse pS {phosphorothioate} at the 5′ terminal 4 bonds of the T7 primerand the SP6 primer so that only final correct product is protected fromT7 exonuclease digestion. The sequence at the junction can be changed byprimer choice. The junction determines the nature of the hairpin cappingthe long RNA helix. Possibilities include a GNRA tetraloop orpotentially a larger loop that can favor the single stranded DNA tohybridize to the long single stranded RNA to produce the desired RNA-DNAhybrid.

To produce the DNA strand of the desired RNA/DNA tethering nucleic acid,the transcription cassette can then be used as a template to performPCR, generally using a thermophilic DNA polymerase. The primers usedinclude a T7 primer and an SP6 primer that has 4×pS (phosphorothioate)bonds at the 5′ terminus. ˜1000 bp double stranded DNA is purified anddigested with T7 exonuclease to completion. The resulting singlestranded DNA will fold back on itself and is optionally purified. Toproduce the RNA strand of the desired RNA/DNA tethering nucleic acid, invitro transcription of the transcription cassette is performed. Highyield kits such as Ambion MegaScript or NEB HiScribe can be used forthese methods, as can other techniques involving T7 RNA polymerase.Following transcription, RNase-free DNase I is added to stop thereaction and degrade the template, EDTA is added, and the product ispurified by acid phenol chloroform extraction and precipitation withammonium acetate and ethanol. The RNA is optionally further purifiedusing methods such as LiCl precipitation and column chromatography (G50)and/or native or denaturing urea-PAGE. Biotin groups may further beadded using methods known in the art, including use of capping guanosinenucleotides. For example, a capping guanosine nucleotide can be added tothe transcript in vitro by a capping enzyme or incorporated as the firstnucleotide during transcription. T7 kits that incorporate a cap arecommercially available. Periodate oxidation can then be used to create acis-diol at both the cap and the 3′ end of the RNA. This diol isunstable and resolves to dual aldehydes. The aldehyde can then bereacted with a biotin-hydrazide (several are commercially available,e.g., Pierce EZ-Link). As another example, a synthetic guanosine capwith a specific reactive moiety (e.g., azide for click chemistry) can beadded to the transcript. Biotin can then be added through an appropriatereaction.

In a further example for creating a tethering nucleic acid, thetethering nucleic acid is a double stranded nucleic acid that has a tagon both ends of a single strand of the duplex. The strand without thetags is then selectively digested and the self-complementary basepairing of the remaining strand causes the strand to fold onto itselfand thereby bring any attached molecules down to the reaction site withit, as is discussed in further detail herein above. One method to createsuch a tagged molecule is to amplify a double stranded DNA moleculeusing a sense and an anti-sense primer designed for these purposes. Thesense primer is designed to have an attachment group at the 5′ end (abisbiotin tag for example). The sequence of the sense primer furtherincludes a recognition site for a nickase that will nick the opposingstrand a few bases upstream from the 3′ end. The primer may also containphosphorothioate or methylphosphonate groups to protect againstdegradation. The antisense primer can be designed to contain a site atthe 5′ end that can be removed but will still leave a 5′ phosphate. Thiscould incorporate a dU for USER excision or a ribo base for RNase or thesame nick site as the other primer, as long as it leaves a 5′ phosphate.The fragment produced by PCR amplification with these primers can betreated with terminal deoxynucleotidyl transferase and a dideoxynucleotide that has the attachment group. This will attach one of theattachment nucleotides to each 3′ end. This is followed by treatmentwith the nickase (and/or USER/RNase) whose sequence was designed intothe primers. This will create both a 5′ and 3′ overhang on the sensestrand and leave a 5′ phosphate on the antisense strand and remove theantisense strand attachment tag. The nicked off bases can be easilyremoved while the main duplex stays bound together. The double strandedduplex is now ready to be loaded into the reaction site (e.g., ZMW) tocapture molecules of interest such as active sequencing complexes. Oncethe complexes have been captured, the non-tagged strand can be removedby a combination of exonucleases. Designing the ssDNA to fold ontoitself will ensure that the complex is rapidly brought to the bottom ofthe ZMW. Lambda exonuclease preferentially degrades dsDNA to ssDNA in a5′->3′ if there is a 5′ phosphate. The 5′ P on the antisense strand willtarget it for degradation and the lack of phosphate (and/or the presenceof phosphorothioates and methylphosphonates) on the 5′ end of the sensestrand will protect it from degradation. The lack of a 5′ phosphate onthe sequencing primer will also protect it if present. Another option isto use Exonuclease III, which preferentially degrades one strand ofdsDNA in a 3′->5′ direction only if there is a blunt end or a 5′overhang. The recessed 3′ end of the antisense strand will target it fordegradation and the 3′ overhang (>4 bases) of the sense strand willprotect it from degradation. The polymerase over the 3′ end of theprimer should protect it from degradation. Polarity of the doublestranded DNA can be designed, for example, by using different tags(attachment chemistries) at each end.

Example 2: Preparing Tethered Nucleic Acid Reagent for Use in GuidewireMethods

An exemplary route for preparing a tethered nucleic acid and using it inaccordance with guidewire methods described herein is schematicallyillustrated in FIG. 17 . This guidewire molecule is generally used toload complexes into deep nanoscale wells. An exemplary DNA moleculeacting as a tether has a self-primed adapter (SP) at one end and anamino-adapter at the other end which can be converted into bis-biotins(or clusters of biotins for even more efficient capture). Thebis-biotins can be protected by a labile streptavidin (SA) (orbisbiotins can be added later to the amino-adapter). The tether DNA isallowed to complex at the SP-adapter with a strand-displacingSA-polymerase (Pol) (e.g., wild type Phi29 Pol-SA, which does not usenucleotide analogs having six phosphate groups (dN6P) forincorporation). This Pol is then locked onto the tethering DNA, e.g.,through reaction of a chemical cross-linker as detailed herein above.This SP-DNA-Pol-SA complex is immobilized at ZMW bottom throughSA-biotin interaction. The locked Pol on the SP-adapter is at the bottomof ZMW while the other DNA end having amino-adapter reaches outside ofthe ZMW or near the entrance. If the amino-adapter was converted intobis-biotins by “click-chemistry” in advance and protected by a labile SAthen dissociation of the labile SA from bis-biotins frees the biotins tointeract. For example, a native (non-labile) SA bound to a polymerasecomplexed with a sequencing template (e.g., a large SMRTbell™) couldcompete with this labile SA. This second polymerase, which will beemployed in sequencing, can be stalled as described above, e.g., usingnon-hydrolyzable dN6P. After capture of the long SMRTbell™-Pol-SAcomplexes by the bisbiotins at the end of the tether DNA, theimmobilized locked WT Pol, binding at the SP adapter of the tether DNA,can start replication when Mg/dNTP is added (+non-hydrolyzable dN6P tomaintain the sequencing polymerase in a stalled state). The replicationaction of this immobilized WT Phi29 Pol, pulling the template throughthe immobilized Pol, allows the amino-adapter end to move down to thebottom of ZMW and pulls the captured stalled SA-Pol-SMRTbell™ complextoward the bottom of ZMW. The locked WT Pol will stop pulling thetethering DNA further when it hits the bisbiotins-SA-Pol-long SMRTbell™complex. At this time, the bisbiotin-captured SA-Pol-long SMRTbell™complex is in the detection zone at the bottom of the ZMW. Thedetectable incorporation of labeled dN6P analogs during replication ofthis captured SA-sequencing Pol can now produce sequencing informationfor the long SMRTbell™.

Example 3: Preparing Tethered Nucleic Acid Reagent for Use inWinching/Fishing Methods

An exemplary route for preparing a tethered nucleic acid for use inWinching/Fishing methods described herein includes the following workflow:

(1) Create the Fishing/Winching Sequence by:

-   -   PCR reaction of a 1-2 kb template with a blunt end restriction        site near one end;    -   add SmrtBell™ hairpins    -   clean up SmrtBell™    -   restriction digest to take one hairpin off to expose sticky end        (although these methods will work with blunt ends as well)    -   ligate on sticky overhang or use existing sticky overhang    -   clean up one hairpin with overhang template    -   anneal primer    -   bind polymerase with excess template to polymerase which        increases the cleanliness of the subsequent sequencing    -   to the primed hairpin add nucleotide lock or covalent polymerase        locking domain or even biotin lock

(2) Create Template molecules by:

-   -   Shear to appropriate size    -   Optional cleanup of fragments    -   Ligate sticky ends compatible with the fishing/winching template        sticky ends (or with optional connector sequence)    -   Size selection    -   Clean up ligated sticky ended templates

(3) Optionally create connector sequence (e.g., about 50-200 bp) withsame sticky ends as on the fishing/winching sequence

(4) Load fishing/winching sequence into ZMW by diffusion loading

(5) Add the template molecules to the loaded ZMW chip plus ligation mixof choice and ligate the templates to the preloaded fishing/winchingsequences; optionally add the connector sequences to make concatemers oftemplates separated by identifiable connectors

(6) After ligation time, wash the chip and load with sequencing mix, hotstart and start observation. Initial sequence will be thefishing/winching template which will pull the ligated template moleculeinto the ZMW and yield the sequence; optionally one could furtherobserve a connecter sequence followed by additional template andconnectors (see FIG. 4 ).

The present specification provides a complete description of themethodologies, systems and/or structures and uses thereof in exampleaspects of the presently-described technology. Although various aspectsof this technology have been described above with a certain degree ofparticularity, or with reference to one or more individual aspects,those skilled in the art could make numerous alterations to thedisclosed aspects without departing from the spirit or scope of thetechnology hereof. Since many aspects can be made without departing fromthe spirit and scope of the presently described technology, theappropriate scope resides in the claims hereinafter appended. Otheraspects are therefore contemplated. Furthermore, it should be understoodthat any operations may be performed in any order, unless explicitlyclaimed otherwise or a specific order is inherently necessitated by theclaim language. It is intended that all matter contained in the abovedescription shall be interpreted as illustrative only of particularaspects and are not limiting to the embodiments shown. Unless otherwiseclear from the context or expressly stated, any concentration valuesprovided herein are generally given in terms of admixture values orpercentages without regard to any conversion that occurs upon orfollowing addition of the particular component of the mixture. To theextent not already expressly incorporated herein, all publishedreferences and patent documents referred to in this disclosure areincorporated herein by reference in their entirety for all purposes.Changes in detail or structure may be made without departing from thebasic elements of the present technology as defined in the followingclaims.

1. A method of delivering a molecule to a site, the method comprising:(a) providing a tethering nucleic acid at the site, wherein at least aportion of the tethering nucleic acid is located outside of the site,wherein the tethering nucleic acid comprises (i) a first strandcomprising a first capture moiety at a position that is located outsideof the site, and (ii) a second strand; (b) exposing the tetheringnucleic acid to a molecule comprising a first binding moiety, whereinthe first binding moiety and the first capture moiety interact to attachthe molecule to the tethering nucleic acid; and (c) degrading the secondstrand of the tethering nucleic acid, wherein the first strand containsself-complementary regions that hybridize together to collapse the firststrand into a hairpin, wherein the collapse of the first strand furtherserves to carry the attached molecule into the interior of the site,thereby delivering the molecule to the site.
 2. The method of claim 1,wherein the first capture moiety comprises biotin and the first bindingmoiety comprises streptavidin.
 3. The method of claim 1, wherein thesecond strand comprises RNA, and wherein in step (c) degrading thesecond strand comprises applying RNAse to the tethering nucleic acid. 4.The method of claim 1, wherein the second strand comprises at least onedeoxyuridine (dU), and wherein in step (c) degrading the second strandcomprises applying uracil-DNA glycosylase and endonuclease VIII to thetethering nucleic acid.
 5. The method of claim 1, wherein the firststrand is resistant to exonuclease and the second strand is sensitive toexonuclease, and wherein in step (c) degrading the second strandcomprises applying an exonuclease to the tethering nucleic acid.
 6. Themethod of claim 1, wherein the molecule is a member selected from thegroup consisting of: a template nucleic acid, a polypeptide, anantibody, and a small molecule.
 7. (canceled)
 8. The method of claim 1,wherein the molecule is part of a complex.
 9. The method of claim 8,wherein the molecule comprises a template nucleic acid complexed with apolymerase enzyme.
 10. The method of claim 9, wherein the complexfurther comprises a primer hybridized to the template nucleic acid. 11.The method of claim 9, wherein the first binding moiety is associatedwith the polymerase enzyme.
 12. The method of claim 1, wherein the firststrand of the tethering nucleic acid comprises the first capture moietyat one end and a second capture moiety at the other end.
 13. (canceled)14. The method of claim 12, wherein the first and second capturemoieties are different.
 15. The method of claim 12, wherein the sitecomprises a second binding moiety, and wherein the tethering nucleicacid is immobilized to the site by an interaction between the secondcapture moiety and the second binding moiety.
 16. The method of claim 1,wherein the tethering nucleic acid is at least 1000 nucleotides inlength.
 17. The method of claim 1, wherein the site comprises a nanoscale well.
 18. The method of claim 1, wherein the site is at the baseof a nanoscale well.
 19. The method of claim 1, wherein the sitecomprises a nanopore.
 20. (canceled)
 21. The method of claim 1, whereinthe method further comprises step (d) immobilizing the molecule to thesite.
 22. The method of claim 21, wherein the immobilizing comprises aninteraction between a first reaction moiety on the site and a secondreaction moiety on the molecule.
 23. (canceled)
 24. The method of claim1, wherein the first capture moiety comprises a scaffold, wherein thescaffold comprises (i) a core comprising conjugation adaptors and (ii)multiple arms comprising biotin moieties. 25-105. (canceled)